ATP5F1A

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0045259 proton-transporting ATP synthase complex	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for CC. ATP5F1A is a core structural component of the proton-transporting ATP synthase complex (Complex V). This is well supported by cryo-EM structural data (PMID:37244256), immunocapture studies (PMID:12110673), and assembly studies (PMID:26297831). Reason: This is the defining complex membership for ATP5F1A. The alpha subunit is one of the major subunits of the F1 catalytic head. Cryo-EM structures show ATP5F1A as chains A/B/C in the alpha3-beta3 hexamer (PMID:37244256). IBA annotation is appropriate and well conserved across the ATPase alpha/beta chains family. Supporting Evidence: PMID:37244256 Biological energy currency ATP is produced by F1Fo-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. PMID:12110673 The immunoprecipitated F(1)F(0) contained a full complement of subunits that were identified with specific antibodies against five of the subunits (alpha, beta, OSCP, d, and IF(1)) file:human/ATP5F1A/ATP5F1A-deep-research-falcon.md ATP5F1A encodes the alpha subunit of the mitochondrial F1 sector of F1FO-ATP synthase (Complex V) in Homo sapiens
GO:0015986 proton motive force-driven ATP synthesis	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for BP. Proton motive force-driven ATP synthesis is the core biological process in which ATP5F1A participates as part of Complex V. While the alpha subunit does not directly catalyze ATP synthesis (that occurs at the beta subunit), it is essential for the process through its structural and regulatory roles. Reason: Correct. ATP5F1A is an essential component of the Complex V machinery that carries out proton motive force-driven ATP synthesis. The alpha subunit provides non-catalytic nucleotide-binding sites that are required for the binding-change mechanism. Well supported by structural evidence (PMID:37244256) and assembly studies (PMID:26297831). Supporting Evidence: PMID:37244256 Biological energy currency ATP is produced by F1Fo-ATP synthase PMID:26297831 Mitochondrial ATP synthase is a motor enzyme in which a central shaft rotates in the stator casings fixed with the peripheral stator stalk.
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for MF with contributes_to qualifier. The alpha subunit contributes to the proton-transporting ATP synthase activity of the holoenzyme complex via the rotational mechanism. The contributes_to qualifier is essential here because ATP5F1A provides non-catalytic nucleotide-binding sites -- the catalytic sites reside on the beta subunit (ATP5F1B). Reason: The contributes_to qualifier is correct and important for the alpha subunit. Unlike the beta subunit which houses the catalytic nucleotide-binding sites, the alpha subunit provides structural support and non-catalytic nucleotide binding required for the rotational mechanism but does not itself catalyze ATP synthesis. UniProt states for P25705: "Subunit alpha does not bear the catalytic high-affinity ATP-binding sites." The rotational mechanism requires the full assembled complex. Supporting Evidence: PMID:37244256 The accommodation of the symmetry mismatch between F1 and Fo motors is resolved by the torsional flexing of the entire complex, especially the gamma subunit, and the rotational substep of the c subunit.
GO:0005524 ATP binding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for MF. ATP binding is well established for the alpha subunit, which has non-catalytic nucleotide-binding sites. Cryo-EM structures (PMID:37244256) show ATP bound at multiple positions on the alpha subunit, and UniProt documents binding residues at positions 215, 217-220, 473, 475 as confirmed by PDB structures 8H9V and 8KI3. Reason: Correct. The alpha subunit binds ATP at its non-catalytic sites. While these are regulatory rather than catalytic binding sites, ATP binding itself is accurately annotated. The term GO:0005524 does not distinguish catalytic from non-catalytic binding, so this is appropriate. Supporting Evidence: PMID:37244256 Biological energy currency ATP is produced by F1Fo-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase
GO:0043531 ADP binding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for MF. ADP binding is a well-established function of the alpha subunit at its non-catalytic nucleotide-binding sites. The alpha subunit binds ADP and ATP at these regulatory sites as part of the binding-change mechanism. Reason: Correct. The alpha subunit has non-catalytic nucleotide-binding sites that bind both ADP and ATP. Well supported phylogenetically and structurally. Supporting Evidence: PMID:37244256 These structures reveal that the release of ADP occurs when the beta subunit of F1Fo-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis
GO:0000166 nucleotide binding	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation for MF based on UniProtKB keyword mapping. Nucleotide binding is correct but very general for ATP5F1A, which specifically binds ATP and ADP at non-catalytic sites. Reason: Correct but broad IEA annotation. The alpha subunit has well-characterized nucleotide (ADP/ATP) binding sites documented by cryo-EM (PMID:37244256). More specific terms like GO:0005524 (ATP binding) and GO:0043531 (ADP binding) are also present in the annotation set, so this broader term is acceptable as an IEA inference. Supporting Evidence: PMID:37244256 Biological energy currency ATP is produced by F1Fo-ATP synthase
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for MF duplicating the IBA annotation for the same GO term. ATP binding is well established for the alpha subunit at its non-catalytic sites. Reason: Correct and consistent with the IBA annotation. Duplicate evidence codes for the same term are fine. UniProt documents ATP binding residues with structural evidence (PDB: 8H9V, 8KI3).
GO:0005739 mitochondrion	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for CC. Mitochondrial localization is well established for ATP5F1A, which has a mitochondrial transit peptide (residues 1-43, UniProt). Reason: Correct. ATP5F1A is a mitochondrial protein with a confirmed transit peptide. Localization to mitochondria is supported by multiple experimental methods and databases.
GO:0005743 mitochondrial inner membrane	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for CC. ATP5F1A is a peripheral membrane protein on the matrix side of the mitochondrial inner membrane, as part of the F1 head of the ATP synthase complex. Reason: Correct. UniProt states ATP5F1A localizes to "Mitochondrion inner membrane; Peripheral membrane protein; Matrix side" with evidence by similarity. The F1 head is attached to the inner membrane via the central and peripheral stalks.
GO:0005886 plasma membrane	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: IEA annotation for CC based on UniProt subcellular location mapping. ATP5F1A is present on the plasma membrane as part of the ecto-ATP synthase complex, documented experimentally by flow cytometry and immunofluorescence (PMID:10077593). Reason: Correct but represents a non-core localization. Plasma membrane localization relates to the ecto-ATP synthase function, which is secondary to the primary mitochondrial localization. Experimentally confirmed by Moser et al. who demonstrated cell surface presence by flow cytometry and immunofluorescence analysis (PMID:10077593). Supporting Evidence: PMID:10077593 The presence of this protein on the cell surface was confirmed by flow cytometry and immunofluorescence analysis.
GO:0006754 ATP biosynthetic process	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation for BP based on UniProt keyword mapping. ATP biosynthetic process is a core function of the ATP synthase complex to which ATP5F1A contributes as a structural and regulatory subunit. Reason: Correct. ATP5F1A is an essential component of Complex V which synthesizes ATP. While the catalytic activity resides in the beta subunit, the alpha subunit is required for the process. This is a broad but accurate term.
GO:0006811 monoatomic ion transport	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation for BP. This term refers to ion transport, which is related to the proton transport function of the ATP synthase complex but is extremely broad. Reason: While very general, this is not incorrect since the F1Fo-ATP synthase complex transports protons (H+) across the inner mitochondrial membrane. ATP5F1A contributes to this function as part of the complex. More specific annotations for proton transport are also present.
GO:0015986 proton motive force-driven ATP synthesis	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for BP based on InterPro mapping. Duplicates the IBA annotation for the same term. Correct. Reason: Correct and consistent with the IBA annotation. Proton motive force-driven ATP synthesis is the core biological process of Complex V. Duplicate evidence from IEA is acceptable.
GO:0016469 proton-transporting two-sector ATPase complex	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation for CC based on ARBA machine learning model. This term describes the broader class of two-sector ATPase complexes (F-type, V-type, A-type). The mitochondrial ATP synthase is an F-type two-sector ATPase. Reason: Correct but general. The F1Fo ATP synthase is indeed a proton-transporting two-sector ATPase complex. More specific annotations for the proton-transporting ATP synthase complex (GO:0045259) are also present. As an IEA from ARBA, the broader term is acceptable.
GO:0032559 adenyl ribonucleotide binding	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for MF based on InterPro mapping. Adenyl ribonucleotide binding includes both ATP and ADP binding, which is correct for the alpha subunit's non-catalytic nucleotide-binding sites. Reason: Correct but broad. The alpha subunit binds adenyl ribonucleotides (ATP and ADP) at its non-catalytic sites. More specific terms (GO:0005524 ATP binding, GO:0043531 ADP binding) are already annotated. As an IEA this broader term is acceptable.
GO:0045259 proton-transporting ATP synthase complex	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for CC, duplicating the IBA annotation for the same GO term. Correct. Reason: Correct and consistent with the IBA annotation. Duplicate evidence codes for the same term are fine.
GO:0046034 ATP metabolic process	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for BP based on InterPro mapping. ATP metabolic process is very broad, encompassing both ATP synthesis and hydrolysis. Reason: Correct but very general. ATP5F1A is involved in ATP metabolism (primarily synthesis as part of Complex V, but the complex can also hydrolyze ATP). More specific annotations for ATP biosynthetic process and proton motive force-driven ATP synthesis are present.
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for MF, duplicating the IBA annotation for the same GO term. Note this IEA lacks the contributes_to qualifier that the IBA has, which is important for the alpha subunit since the catalytic activity resides in the beta subunit. Reason: Correct term but ideally should have the contributes_to qualifier as in the IBA annotation. For the alpha subunit, which provides non-catalytic nucleotide-binding sites, the contributes_to qualifier is particularly important. However, as an IEA the absence of the qualifier is a minor issue.
GO:1902495 transmembrane transporter complex	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation for CC based on ARBA. The ATP synthase complex is a transmembrane transporter complex that translocates protons across the membrane. Reason: Correct but very general. The F1Fo-ATP synthase is indeed a transmembrane transporter complex. More specific terms (GO:0045259, GO:0016469) are also annotated.
GO:1902600 proton transmembrane transport	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for BP. Proton transmembrane transport is a core process of the ATP synthase complex. Reason: Correct. The F1Fo-ATP synthase transports protons across the inner mitochondrial membrane as part of its catalytic cycle. ATP5F1A contributes to this as a structural subunit of the F1 head.
GO:0005515 protein binding	IPI PMID:11410595 Atp11p and Atp12p are assembly factors for the F(1)-ATPase i...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from a study demonstrating that Atp11p and Atp12p (ATPAF1/ATPAF2) are assembly factors for F1-ATPase in human mitochondria (Wang et al. 2001). UniProt confirms the interaction with ATPAF2 (PubMed:11410595). This is a specific, functionally characterized interaction with an assembly chaperone. Reason: The interaction with ATPAF2 is specific and functionally meaningful -- ATPAF2 is a dedicated assembly factor for ATP5F1A. However, the generic "protein binding" term is uninformative. A more specific term capturing the chaperone/assembly factor interaction would be preferable, but such a term may not exist in GO. Supporting Evidence: PMID:11410595 Atp11p and Atp12p were first described as proteins required for assembly of the F(1) component of the mitochondrial ATP synthase in Saccharomyces cerevisiae
GO:0005515 protein binding	IPI PMID:15161933 Comprehensive proteomic analysis of interphase and mitotic 1...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from a large-scale proteomic analysis of 14-3-3-binding proteins (Meek et al. 2004). ATP5F1A was identified as a 14-3-3-binding protein in HeLa cells. Reason: This is a high-throughput proteomic study identifying many 14-3-3-binding proteins. While the interaction may be real, the generic "protein binding" term is uninformative and the biological significance of 14-3-3 binding to ATP5F1A is not characterized. Supporting Evidence: PMID:15161933 Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding proteins.
GO:0005515 protein binding	IPI PMID:15324660 Proteomic, functional, and domain-based analysis of in vivo ...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from another 14-3-3-binding protein study (Jin et al. 2004). Focused on cytoskeletal regulation and cellular organization. Reason: High-throughput 14-3-3 interaction proteomics study. Generic protein binding is uninformative. The biological relevance to ATP5F1A function is unclear. Supporting Evidence: PMID:15324660 Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization.
GO:0005515 protein binding	IPI PMID:19343720 Identification and characterization of proteins interacting ...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from a study identifying proteins interacting with SIRT1 and SIRT3 (Law et al. 2009). UniProt confirms SIRT3 interaction with ATP5F1A. SIRT3 is a mitochondrial deacetylase that regulates the acetylation of OXPHOS components. Reason: While the SIRT3 interaction is biologically meaningful (SIRT3 deacetylates ATP5F1A as part of mitochondrial metabolic regulation), the generic "protein binding" term is uninformative. A more specific term would be preferable. Supporting Evidence: PMID:19343720 Identification and characterization of proteins interacting with SIRT1 and SIRT3
GO:0005515 protein binding	IPI PMID:19688755 LC-MS/MS as an alternative for SDS-PAGE in blue native analy...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from an LC-MS/MS study analyzing protein complexes by blue native analysis (Wessels et al. 2009). This likely detected ATP5F1A as part of intact Complex V. Reason: Large-scale proteomic study. The detection of ATP5F1A in protein complexes is expected given that it is a subunit of Complex V. Generic protein binding is uninformative. Supporting Evidence: PMID:19688755 LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes.
GO:0005515 protein binding	IPI PMID:20618440 Proteomic and biochemical analysis of 14-3-3-binding protein...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from proteomic analysis of 14-3-3-binding proteins during C2-ceramide-induced apoptosis (Pozuelo-Rubio 2010). Reason: Another 14-3-3 interaction proteomics study. Generic protein binding is uninformative. The biological relevance to ATP5F1A function is unclear. Supporting Evidence: PMID:20618440 Proteomic and biochemical analysis of 14-3-3-binding proteins during C2-ceramide-induced apoptosis.
GO:0005515 protein binding	IPI PMID:22309213 Identification of a molecular component of the mitochondrial...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from a study identifying GCN5L1 (BLOC1S1) as a mitochondrial acetyltransferase component (Scott et al. 2012). UniProt confirms that ATP5F1A interacts with BLOC1S1 and that BLOC1S1 is required for acetylation of ATP5F1A. BLOC1S1 promotes acetylation of SIRT3 respiratory chain targets. Reason: The interaction with BLOC1S1/GCN5L1 is biologically meaningful for mitochondrial acetylation regulation, but the generic "protein binding" term is uninformative. The study showed that GCN5L1 interacts with and promotes acetylation of respiratory chain targets, including ATP5F1A. Supporting Evidence: PMID:22309213 GCN5L1 interacts with and promotes acetylation of SIRT3 respiratory chain targets and reverses global SIRT3 effects on mitochondrial protein acetylation, respiration and bioenergetics.
GO:0005515 protein binding	IPI PMID:27499296 Mitochondrial Protein Interaction Mapping Identifies Regulat...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from mitochondrial protein interaction mapping study (Floyd et al. 2016). Focused mitochondrial interactome study identifying regulators of respiratory chain function. Reason: While this is a mitochondria-focused interaction study, the generic protein binding term is uninformative. The study mapped mitochondrial protein interactions but the specific functional significance for ATP5F1A is not captured by this annotation. Supporting Evidence: PMID:27499296 Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function.
GO:0005515 protein binding	IPI PMID:28514442 Architecture of the human interactome defines protein commun...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from a large-scale human interactome mapping study (Huttlin et al. 2017). High-throughput study mapping the architecture of the human interactome. Reason: Large-scale interactome study. Generic protein binding is uninformative for a well-characterized enzyme subunit. Supporting Evidence: PMID:28514442 Architecture of the human interactome defines protein communities and disease networks.
GO:0005515 protein binding	IPI PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Ma...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from a histone interaction landscape study using crosslinking mass spectrometry in intact cell nuclei (Fasci et al. 2018). ATP5F1A detected as a histone-interacting protein. Reason: This study focused on histone interactions by crosslinking mass spectrometry. Detection of ATP5F1A likely reflects its abundance rather than a specific functional interaction with histones. Generic protein binding is uninformative. Supporting Evidence: PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from interactome mapping focused on neurodegenerative disease proteins (Haenig et al. 2020). UniProt documents an interaction with HTT (huntingtin). Reason: Disease-focused interactome study. Generic protein binding is uninformative. The interaction with neurodegenerative disease proteins is likely not a core function of ATP5F1A. Supporting Evidence: PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
GO:0005515 protein binding	IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from dual proteome-scale network study showing cell-specific remodeling of the human interactome (Huttlin et al. 2021). Reason: Large-scale interactome study. Generic protein binding is uninformative. Supporting Evidence: PMID:33961781 Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks.
GO:0005515 protein binding	IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from multimodal cell maps study (2024). High-throughput study mapping structural and functional genomics. Reason: Large-scale high-throughput study. Generic protein binding is uninformative for ATP5F1A. Supporting Evidence: PMID:40205054 Multimodal cell maps as a foundation for structural and functional genomics.
GO:0002020 protease binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: IEA annotation for MF based on Ensembl Compara ortholog transfer. Protease binding may relate to the interaction with angiostatin, a proteolytic fragment of plasminogen, which binds the alpha subunit on the cell surface (PMID:10077593). Reason: This likely derives from the ecto-ATP synthase function where the alpha subunit binds angiostatin (a protease fragment of plasminogen) on the cell surface. While the interaction is experimentally documented (PMID:10077593), this is a secondary function associated with ecto-ATP synthase, not the core mitochondrial role. Supporting Evidence: PMID:10077593 Angiostatin binds ATP synthase on the surface of human endothelial cells
GO:0009986 cell surface	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: IEA annotation for CC based on Ensembl Compara. ATP5F1A is present on the cell surface as part of ecto-ATP synthase, demonstrated by flow cytometry and immunofluorescence (PMID:10077593). Reason: Correct but represents a non-core localization. Cell surface presence relates to the ecto-ATP synthase function. Primary localization is mitochondrial. Experimentally supported by Moser et al. (PMID:10077593). Supporting Evidence: PMID:10077593 The presence of this protein on the cell surface was confirmed by flow cytometry and immunofluorescence analysis.
GO:0014850 response to muscle activity	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: IEA annotation for BP from Ensembl Compara ortholog transfer. This is a pleiotropic response annotation likely transferred from a model organism where ATP5F1A expression changes with muscle activity. Reason: While mitochondrial ATP synthase subunit expression could reasonably be modulated by muscle activity (given the high energy demand of muscle), this is a downstream response rather than a core function of ATP5F1A. It reflects the metabolic adaptation of the OXPHOS system to energy demands.
GO:0016020 membrane	IEA GO_REF:0000107	ACCEPT	Summary: IEA annotation for CC from Ensembl Compara. Very broad term. ATP5F1A associates with multiple membranes (mitochondrial inner membrane, plasma membrane as ecto-ATP synthase). Reason: Correct but very broad. ATP5F1A is a peripheral membrane protein associated with the mitochondrial inner membrane and cell surface membrane. More specific terms are annotated elsewhere.
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000107	ACCEPT	Summary: IEA annotation for MF with contributes_to qualifier from Ensembl Compara. ATP hydrolysis is the reverse activity of ATP synthase, which can be activated in vitro. UniProt notes that in vivo the enzyme can only synthesize ATP, but its ATP hydrolase activity can be activated artificially in vitro. Reason: The contributes_to qualifier is appropriate. The Complex V can hydrolyze ATP (the reverse reaction) and this is regulated by IF1 (ATPIF1). The alpha subunit contributes to this activity as part of the complex. UniProt states: "In vivo, can only synthesize ATP although its ATP hydrolase activity can be activated artificially in vitro." The immunocapture study (PMID:12110673) directly measured ATP hydrolysis activity of the purified complex. Supporting Evidence: PMID:12110673 The captured complex V displayed ATP hydrolysis activity that was fully oligomycin and inhibitor protein IF(1)-sensitive.
GO:0043531 ADP binding	IEA GO_REF:0000107	ACCEPT	Summary: IEA annotation for MF from Ensembl Compara, duplicating the IBA annotation for the same GO term. Reason: Correct and consistent with the IBA annotation. Duplicate evidence codes are fine. The alpha subunit binds ADP at its non-catalytic nucleotide-binding sites.
GO:0045121 membrane raft	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: IEA annotation for CC from Ensembl Compara. Membrane raft localization may relate to the ecto-ATP synthase function on the cell surface. Reason: This likely relates to the ecto-ATP synthase localization in lipid raft/membrane raft domains on the cell surface, which has been documented for ATP synthase subunits (PMID:17643490 shows co-localization with MHC-I in punctate membrane domains). This is a secondary localization associated with the ecto function. Supporting Evidence: PMID:17643490 Confocal microscopy analysis of MHC-I and ecto-F1-ATPase beta chain expression on HepG2 cells shows a co-localization of both complexes in punctate membrane domains.
GO:0045471 response to ethanol	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: IEA annotation for BP from Ensembl Compara ortholog transfer. This is a broad response annotation likely reflecting that ATP synthase expression is modulated by ethanol exposure. Reason: Ethanol affects mitochondrial function and OXPHOS complex expression, so ATP5F1A expression changes in response to ethanol are plausible but represent a downstream effect rather than a core function. This is a pleiotropic response annotation.
GO:0071549 cellular response to dexamethasone stimulus	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: IEA annotation for BP from Ensembl Compara. Dexamethasone can modulate mitochondrial function and gene expression, including OXPHOS components. Reason: Pleiotropic response annotation. Dexamethasone effects on ATP5F1A expression are a secondary consequence of glucocorticoid signaling on mitochondrial metabolism, not a core function.
GO:0071732 cellular response to nitric oxide	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: IEA annotation for BP from Ensembl Compara. Nitric oxide is known to inhibit mitochondrial respiration and can modify Complex V. Reason: Pleiotropic response annotation. NO affects mitochondrial OXPHOS function, and Complex V subunit expression or modification may change in response. This is a downstream effect, not a core function of ATP5F1A.
GO:0005739 mitochondrion	IDA GO_REF:0000052	ACCEPT	Summary: IDA annotation for CC based on curation of immunofluorescence data. Mitochondrial localization confirmed by immunofluorescence. Reason: Correct. Direct experimental evidence for mitochondrial localization via immunofluorescence. This is the primary localization for ATP5F1A.
GO:0005743 mitochondrial inner membrane	NAS PMID:26297831 Assembly of human mitochondrial ATP synthase through two sep...	ACCEPT	Summary: NAS annotation for CC citing the assembly study of human mitochondrial ATP synthase (Fujikawa et al. 2015). The study demonstrates that alpha subunits assemble into the F1-c-ring intermediate at the inner mitochondrial membrane. Reason: Correct. The alpha subunit is part of the F1 head which is attached to the inner mitochondrial membrane via the central stalk connected to the Fo sector. The assembly study shows that F1 (containing alpha subunits) assembles with the c-ring as an intermediate (PMID:26297831). Supporting Evidence: PMID:26297831 When expression of d-subunit, a stator stalk component, was knocked-down, human cells could not form ATP synthase holocomplex and instead accumulated two subcomplexes, one containing a central rotor shaft plus catalytic subunits (F1-c-ring)
GO:0015986 proton motive force-driven ATP synthesis	NAS PMID:26297831 Assembly of human mitochondrial ATP synthase through two sep...	ACCEPT	Summary: NAS annotation for BP citing the assembly study. The study addresses assembly of the ATP synthase rather than directly demonstrating the proton motive force-driven ATP synthesis activity, but the function is well established. Reason: While the cited study focuses on assembly, proton motive force-driven ATP synthesis is the core function of the complex that ATP5F1A assembles into. Well supported by other references. Supporting Evidence: PMID:26297831 Mitochondrial ATP synthase is a motor enzyme in which a central shaft rotates in the stator casings fixed with the peripheral stator stalk.
GO:0015986 proton motive force-driven ATP synthesis	IDA PMID:37244256 Structure of the human ATP synthase.	ACCEPT	Summary: IDA annotation for BP from the cryo-EM structure of human ATP synthase (Lai et al. 2023). The study resolved multiple rotational states demonstrating the proton motive force-driven ATP synthesis mechanism, with ATP5F1A visible as chains A/B/C. Reason: Correct. The structural study directly visualizes the rotary mechanism of ATP synthesis in the human enzyme, with the alpha subunit forming part of the catalytic hexameric head. Represents core function. Supporting Evidence: PMID:37244256 Biological energy currency ATP is produced by F1Fo-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase
GO:0045259 proton-transporting ATP synthase complex	IDA PMID:37244256 Structure of the human ATP synthase.	ACCEPT	Summary: IDA annotation for CC from the cryo-EM structure of human ATP synthase. The study directly resolved ATP5F1A as part of the intact complex. Reason: Direct structural evidence. The cryo-EM structure (PDB: 8H9E and others) shows ATP5F1A as chains A/B/C in the intact human ATP synthase complex. Supporting Evidence: PMID:37244256 Structure of the human ATP synthase
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	ACCEPT	Summary: HTP annotation for CC from the quantitative high-confidence human mitochondrial proteome study (Morgenstern et al. 2021). ATP5F1A was identified with high confidence as part of the mitochondrial proteome. Reason: Correct. This high-quality mitochondrial proteomics study provides strong quantitative evidence for mitochondrial localization. ATP5F1A is one of the most abundant mitochondrial proteins. Supporting Evidence: PMID:34800366 We classified >8,000 proteins in mitochondrial preparations of human cells and defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP).
GO:0005739 mitochondrion	IC PMID:12110673 A functionally active human F1F0 ATPase can be purified by i...	ACCEPT	Summary: IC annotation for CC citing the immunocapture study (Aggeler et al. 2002). ATP5F1A was identified as a subunit of immunocaptured F1Fo from heart tissue and fibroblasts. Reason: Correct. The immunocapture study isolated F1Fo from mitochondria, confirming the alpha subunit is a mitochondrial protein. The study identified ATP5F1A with specific antibodies. Supporting Evidence: PMID:12110673 The immunoprecipitated F(1)F(0) contained a full complement of subunits that were identified with specific antibodies against five of the subunits (alpha, beta, OSCP, d, and IF(1))
GO:0045259 proton-transporting ATP synthase complex	IDA PMID:12110673 A functionally active human F1F0 ATPase can be purified by i...	ACCEPT	Summary: IDA annotation for CC from the immunocapture study. ATP5F1A was directly identified as a component of the purified ATP synthase complex from heart tissue and fibroblasts. Reason: Direct experimental evidence. The alpha subunit was identified by specific antibodies in the immunocaptured F1Fo complex. Supporting Evidence: PMID:12110673 The immunoprecipitated F(1)F(0) contained a full complement of subunits that were identified with specific antibodies against five of the subunits (alpha, beta, OSCP, d, and IF(1))
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	IDA PMID:12110673 A functionally active human F1F0 ATPase can be purified by i...	ACCEPT	Summary: IDA annotation for MF with contributes_to qualifier from the immunocapture study. The purified complex containing the alpha subunit displayed ATP hydrolysis activity (the reverse of ATP synthesis via the rotational mechanism), confirming the complex is functional. Reason: Correct. The contributes_to qualifier is appropriate since the alpha subunit contributes to but does not itself catalyze the activity. The study directly measured ATP hydrolysis activity of the immunocaptured complex. Supporting Evidence: PMID:12110673 The captured complex V displayed ATP hydrolysis activity that was fully oligomycin and inhibitor protein IF(1)-sensitive.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-164832	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "ATPase synthesizes ATP". The F1 head where ATP5F1A resides faces the mitochondrial matrix. Reason: Correct. The F1 catalytic head, containing the alpha3-beta3 hexamer, faces the mitochondrial matrix. ATP5F1A is a matrix-exposed peripheral membrane protein.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-164834	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "Enzyme-bound ATP is released". Duplicate CC annotation from a different Reactome reaction. Correct. Reason: Correct. Same localization from a different Reactome reaction in the ATP synthesis pathway. The alpha subunit is in the matrix-facing F1 head.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-164840	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "ADP and Pi bind to ATPase". Duplicate CC annotation from a different Reactome reaction. Correct. Reason: Correct. Same localization from another Reactome reaction step. ADP and Pi binding occurs in the matrix-facing catalytic head.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-8949580	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "F1Fo ATP synthase dimerizes". The dimerization occurs at the inner mitochondrial membrane, with the F1 head in the matrix. Reason: Correct. ATP synthase dimerization is relevant to cristae formation and the alpha subunit is located in the matrix.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838035	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "CLPXP binds mitochondrial matrix proteins". ATP5F1A is a substrate of CLPXP protease in the mitochondrial matrix. Reason: Correct. ATP5F1A is a mitochondrial matrix-exposed protein that is recognized by CLPXP as a substrate for quality control/degradation.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838081	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "LONP1 degrades mitochondrial matrix proteins". ATP5F1A is a substrate of LONP1 protease in the matrix. Reason: Correct. The matrix-facing F1 head exposes ATP5F1A to matrix proteases like LONP1 for quality control.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838093	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "LONP1 binds mitochondrial matrix proteins". Same context as above. Reason: Correct. Duplicate CC annotation from the LONP1 binding step. ATP5F1A is in the mitochondrial matrix.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838289	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "CLPXP degrades mitochondrial matrix proteins". Reason: Correct. Same localization from the CLPXP degradation reaction.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9839105	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "AFG3L2 degrades mitochondrial matrix proteins". Reason: Correct. ATP5F1A is exposed to matrix-side proteases for quality control.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9839149	ACCEPT	Summary: TAS annotation for CC from Reactome pathway "AFG3L2 binds mitochondrial matrix proteins". Reason: Correct. Same mitochondrial matrix localization from the AFG3L2 binding step.
GO:0006754 ATP biosynthetic process	IMP PMID:21106936 Regenerative protein thymosin beta-4 is a novel regulator of...	ACCEPT	Summary: IMP annotation for BP from the thymosin beta-4 study (Freeman et al. 2011). The study showed that thymosin beta-4 increases cell surface ATP levels via ATP synthase, demonstrating ATP biosynthetic process. Although evidence comes from ecto-ATP synthase, the GO term (ATP biosynthetic process) describes a core function of ATP5F1A. Reason: The GO term GO:0006754 is correct for ATP5F1A. While the evidence comes from the ecto-ATP synthase context, ATP biosynthetic process is a core function of the gene. Consistent with IEA and NAS annotations to the same term. Supporting Evidence: PMID:21106936 we have identified an extracellular signaling pathway where Tβ4 increases cell surface ATP levels via ATP synthase
GO:0043536 positive regulation of blood vessel endothelial cell migration	IGI PMID:21106936 Regenerative protein thymosin beta-4 is a novel regulator of...	KEEP AS NON CORE	Summary: IGI annotation for BP from the thymosin beta-4 study. The study showed that thymosin beta-4 promotes HUVEC migration through ecto-ATP synthase, with ATP-responsive P2X4 receptor required for the migration effect. ATP5F1A participates as part of the ecto-ATP synthase complex. Reason: This is a downstream effect of ecto-ATP synthase function. While the interaction is experimentally demonstrated, positive regulation of endothelial cell migration is mediated through extracellular ATP/purinergic signaling and is a non-core function of ATP5F1A. Supporting Evidence: PMID:21106936 Silencing of the ATP-responsive purinergic receptor P2X4 with siRNA also blocked Tβ4-induced HUVEC migration in a transwell assay.
GO:0042776 proton motive force-driven mitochondrial ATP synthesis	IDA PMID:12110673 A functionally active human F1F0 ATPase can be purified by i...	ACCEPT	Summary: IDA annotation for BP from the immunocapture study (Aggeler et al. 2002). The purified complex containing ATP5F1A was functionally active with ATP hydrolysis (reverse of synthesis), demonstrating the complex's catalytic capability. Reason: Correct. This is the most specific BP annotation for ATP5F1A's core function. The immunocapture study isolated functional F1Fo from human heart tissue and fibroblasts, containing the alpha subunit, and demonstrated catalytic activity. While the alpha subunit is the non-catalytic subunit, it is essential for the process. Supporting Evidence: PMID:12110673 The captured complex V displayed ATP hydrolysis activity that was fully oligomycin and inhibitor protein IF(1)-sensitive.
GO:0045259 proton-transporting ATP synthase complex	IDA PMID:21106936 Regenerative protein thymosin beta-4 is a novel regulator of...	ACCEPT	Summary: IDA annotation for CC from the thymosin beta-4 study. The study identified F1-F0 ATP synthase as a target of thymosin beta-4 by pulldown and mass spectrometry, with ATP5F1A as part of the complex. Reason: Correct. The study directly identified F1-F0 ATP synthase components by mass spectrometry, confirming ATP5F1A as a complex member. Supporting Evidence: PMID:21106936 we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	IMP PMID:21106936 Regenerative protein thymosin beta-4 is a novel regulator of...	ACCEPT	Summary: IMP annotation for MF from the thymosin beta-4 study (Freeman et al. 2011). The study showed that oligomycin (an ATP synthase inhibitor) blocked the thymosin beta-4-induced increase in cell surface ATP levels, demonstrating ATP synthase activity. Although the evidence comes from ecto-ATP synthase on the cell surface, the GO term itself (proton- transporting ATP synthase activity, rotational mechanism) is a core function of ATP5F1A. Reason: The GO term GO:0046933 is correct for ATP5F1A regardless of whether evidence comes from mitochondrial or ecto-ATP synthase context. The term describes the molecular activity of the complex, which is a core function. The alpha subunit contributes to this activity via non-catalytic nucleotide binding sites. Consistent with IBA, IEA, IDA, and ISS annotations to the same term. Supporting Evidence: PMID:21106936 Blocking antibodies and antagonists (oligomycin, IC(50) ∼1.8 μM; piceatannol, IC(50) ∼1.05 μM; and angiostatin, IC(50) ∼2.9 μg/ml) of ATP synthase inhibited the Tβ4-induced increase in cell surface ATP levels, as measured by luciferase assay, and the Tβ4-induced increase in HUVEC migration, as measured by transwell migration assay
GO:0005515 protein binding	IPI PMID:21106936 Regenerative protein thymosin beta-4 is a novel regulator of...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from the thymosin beta-4 study. The study identified the interaction between thymosin beta-4 and F1-F0 ATP synthase by pulldown experiments. However, the binding was specifically to the beta subunit (K_D 12 nM), not the alpha subunit. Reason: The study primarily demonstrates thymosin beta-4 binding to the beta subunit of ATP synthase (K_D 12 nM by SPR). The alpha subunit was co-isolated as part of the complex but was not shown to be the direct binding partner. Generic protein binding is uninformative. Supporting Evidence: PMID:21106936 By surface plasmon resonance, we determined for Tβ4 binding to the β subunit of ATP synthase a K(D) of 12 nM.
GO:0016020 membrane	IDA PMID:21106936 Regenerative protein thymosin beta-4 is a novel regulator of...	ACCEPT	Summary: IDA annotation for CC from the thymosin beta-4 study. This likely refers to the cell surface membrane where ecto-ATP synthase is found. Reason: Correct. ATP5F1A is associated with membranes -- both the mitochondrial inner membrane and the plasma membrane (as ecto-ATP synthase). Very broad but acceptable. Supporting Evidence: PMID:21106936 we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin
GO:0043532 angiostatin binding	IPI PMID:21106936 Regenerative protein thymosin beta-4 is a novel regulator of...	KEEP AS NON CORE	Summary: IPI annotation for MF from the thymosin beta-4 study. However, this annotation appears incorrectly attributed to this reference. The original angiostatin binding to ATP5F1A was demonstrated in PMID:10077593 (Moser et al. 1999), where angiostatin was shown to bind the alpha/beta subunits of ATP synthase on the cell surface. Reason: Angiostatin binding to ATP5F1A is well documented (PMID:10077593) and confirmed by multiple studies. However, it is a non-core function related to ecto-ATP synthase. The referenced study (PMID:21106936) does mention angiostatin as an ATP synthase antagonist but the primary evidence for angiostatin binding to the alpha subunit comes from PMID:10077593. Supporting Evidence: PMID:10077593 Angiostatin also bound to the recombinant alpha-subunit of human ATP synthase, and this binding was not inhibited by a 2,500-fold molar excess of plasminogen. PMID:21106936 we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin
GO:0005515 protein binding	IPI PMID:11741979 Interaction of the C-terminal domain of p43 and the alpha su...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from the p43/EMAP II study (Chang et al. 2002). The study demonstrated that EMAP II (C-terminal domain of p43) binds the alpha subunit of ATP synthase on the cell surface and inhibits endothelial cell proliferation. Reason: The interaction with EMAP II is specific and functionally characterized (EMAP II binds cell-surface alpha-ATP synthase and inhibits endothelial cell growth). However, the generic "protein binding" term is uninformative. This is also a non-core ecto-ATP synthase function. Supporting Evidence: PMID:11741979 The isolated protein was determined to be the alpha subunit of ATP synthase. The interaction of EMAP II and alpha-ATP synthase was confirmed by enzyme-linked immunosorbent assay and in vitro pull down assays
GO:0070062 extracellular exosome	HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres...	KEEP AS NON CORE	Summary: HDA annotation for CC from in-depth proteomic analysis of exosomes isolated from expressed prostatic secretions in urine. ATP5F1A was identified in exosomal fractions. Reason: Detection of ATP5F1A in extracellular exosomes is consistent with its abundance and the known presence of mitochondrial proteins in exosomes. This is a non-core localization. Supporting Evidence: PMID:23533145 In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.
GO:0016020 membrane	HDA PMID:19946888 Defining the membrane proteome of NK cells.	ACCEPT	Summary: HDA annotation for CC from a study defining the membrane proteome of NK cells. ATP5F1A was identified in the membrane fraction. Reason: Correct. ATP5F1A is a membrane-associated protein (mitochondrial inner membrane and potentially cell surface). Detection in the membrane proteome is expected. Supporting Evidence: PMID:19946888 Defining the membrane proteome of NK cells.
GO:0003723 RNA binding	HDA PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-bi...	MARK AS OVER ANNOTATED	Summary: HDA annotation for MF from the mammalian mRNA-binding protein atlas study (Castello et al. 2012). ATP5F1A was detected as an mRNA-binding protein in this large-scale UV crosslinking study. Reason: This is from a large-scale UV crosslinking study that identified thousands of mRNA-binding proteins. Many abundant proteins are detected in such screens due to non-specific crosslinking. RNA binding is not a characterized function of ATP5F1A and is likely an artifact of the protein's high abundance. Supporting Evidence: PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.
GO:0005739 mitochondrion	HDA PMID:20833797 Phosphoproteome analysis of functional mitochondria isolated...	ACCEPT	Summary: HDA annotation for CC from a phosphoproteome analysis of functional mitochondria isolated from resting human muscle (Zhao et al. 2011). ATP5F1A was identified as a phosphorylated mitochondrial protein. Reason: Correct. ATP5F1A was identified in functional mitochondria from human muscle, consistent with its well-established mitochondrial localization and known phosphorylation sites (UniProt documents multiple phosphoserine sites). Supporting Evidence: PMID:20833797 We performed a phosphoproteomics study of functional mitochondria isolated from human muscle biopsies
GO:0070062 extracellular exosome	HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos...	KEEP AS NON CORE	Summary: HDA annotation for CC from large-scale proteomics and phosphoproteomics of urinary exosomes. ATP5F1A was identified in exosomal fractions. Reason: Detection in urinary exosomes is consistent with the abundance of ATP5F1A and the known presence of mitochondrial proteins in exosomal fractions. Non-core localization. Supporting Evidence: PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exosomes.
GO:0005515 protein binding	IPI PMID:19285951 High affinity interaction between histidine-rich glycoprotei...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from a study demonstrating that histidine-rich glycoprotein (HRG) interacts with the alpha subunit of ATP synthase on the surface of T-cells (Ohta et al. 2009). The interaction was specific (K_D 66 nM) and mediates HRG/Con A-induced morphological changes. Reason: The HRG-ATP5F1A interaction is specific and well-characterized (K_D 66 nM). However, generic "protein binding" is uninformative. This is an ecto-ATP synthase interaction. UniProt confirms: "Interacts with HRG; the interaction occurs on the surface of T-cells." Supporting Evidence: PMID:19285951 HRG specifically interacted with mitochondrial ATP synthase with a dissociation constant of 66 nM.
GO:0005743 mitochondrial inner membrane	IDA PMID:19016746 Identification of mitochondrial F(1)F(0)-ATP synthase intera...	ACCEPT	Summary: IDA annotation for CC from a study identifying galectin-3 interaction with mitochondrial F1F0-ATP synthase in colon cancer cells (Kim et al. 2008). The study showed that galectin-3 and ATP synthase co-localized in the inner membrane vesicles of mitochondria. Reason: Correct. The study demonstrated by subcellular fractionation that ATP synthase is in the inner mitochondrial membrane, co-localized with galectin-3. Supporting Evidence: PMID:19016746 Galectin-3 and ATP synthase were co-isolated in the inner membrane vesicles of mitochondria.
GO:0005524 ATP binding	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation for MF based on manual transfer from ortholog by curator judgment. ATP binding is well established for the alpha subunit at its non-catalytic nucleotide-binding sites. Reason: Correct. The alpha subunit binds ATP at non-catalytic regulatory sites. Well supported by structural evidence (PMID:37244256) and UniProt binding site annotations.
GO:0005739 mitochondrion	NAS PMID:1830491 Nucleotide sequence of a cDNA for the alpha subunit of human...	ACCEPT	Summary: NAS annotation for CC citing the original cDNA cloning paper for the alpha subunit (Kataoka & Biswas 1991). The paper describes cloning the cDNA for the alpha subunit of human mitochondrial ATP synthase. Reason: Correct. The original cloning paper established the identity of this gene as encoding the alpha subunit of mitochondrial ATP synthase. Supporting Evidence: PMID:1830491 A full length cDNA clone of the alpha subunit of mitochondrial ATP synthase (EC 3.6.1.34) has been isolated from a cDNA library prepared from LX-1 human tumor cells
GO:0006629 lipid metabolic process	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS annotation for BP based on ortholog transfer. Lipid metabolic process may relate to the ecto-ATP synthase role in HDL/apolipoprotein metabolism, where cell surface ATP synthase is involved in HDL endocytosis. Reason: This likely refers to the ecto-ATP synthase function in HDL metabolism. Cell-surface ATP synthase has been implicated in apolipoprotein A-I-stimulated HDL endocytosis in hepatocytes. While this is a legitimate function, it is secondary to the core mitochondrial role.
GO:0006754 ATP biosynthetic process	NAS PMID:1830491 Nucleotide sequence of a cDNA for the alpha subunit of human...	ACCEPT	Summary: NAS annotation for BP citing the original cDNA cloning paper. The paper describes ATP5F1A as a subunit of mitochondrial ATP synthase, implying its role in ATP biosynthesis. Reason: Correct. The original paper identified this gene as encoding a subunit of ATP synthase (EC 3.6.1.34), which is responsible for ATP biosynthesis. Supporting Evidence: PMID:1830491 A full length cDNA clone of the alpha subunit of mitochondrial ATP synthase (EC 3.6.1.34) has been isolated
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation for MF based on ortholog transfer. The proton-transporting ATP synthase activity is well established for this complex. Note this annotation lacks the contributes_to qualifier that is appropriate for the alpha subunit. Reason: Correct term. Ideally should have the contributes_to qualifier for the alpha subunit since catalytic activity resides in the beta subunit, but as an ISS the annotation is acceptable.
GO:0042288 MHC class I protein binding	IDA PMID:17643490 Ecto-F1-ATPase and MHC-class I close association on cell mem...	KEEP AS NON CORE	Summary: IDA annotation for MF from the study showing close association between ecto-F1-ATPase and MHC class I on cell membranes (Vantourout et al. 2008). The study demonstrated that biotinylated F1-ATPase cell surface components co-immunoprecipitate with MHC-I molecules and co-localize in punctate membrane domains. Reason: This is a specific and experimentally supported annotation related to the ecto-ATP synthase function. MHC class I association is relevant to immune recognition (gamma/delta T cell activation) and represents a specialized function on the cell surface. Non-core relative to the primary mitochondrial function. Supporting Evidence: PMID:17643490 biotinylated F1-ATPase cell surface components co-immunoprecipitate with MHC-I molecules confirming the association of both complexes on Raji cells. Confocal microscopy analysis of MHC-I and ecto-F1-ATPase beta chain expression on HepG2 cells shows a co-localization of both complexes in punctate membrane domains.
GO:0001937 negative regulation of endothelial cell proliferation	IMP PMID:10077593 Angiostatin binds ATP synthase on the surface of human endot...	KEEP AS NON CORE	Summary: IMP annotation for BP from the angiostatin binding study (Moser et al. 1999). The study showed that angiostatin binding to ATP synthase alpha/beta subunits on the cell surface mediates its antiproliferative effect, which was inhibited by anti-alpha-subunit antibody. Reason: This is a well-documented ecto-ATP synthase function. Angiostatin binding to cell surface ATP5F1A mediates inhibition of endothelial cell proliferation. However, this is a non-core function related to the ecto-ATP synthase role, not the primary mitochondrial function. Supporting Evidence: PMID:10077593 Angiostatin's antiproliferative effect on endothelial cells was inhibited by as much as 90% in the presence of anti-alpha-subunit ATP synthase antibody.
GO:0005886 plasma membrane	IDA PMID:10077593 Angiostatin binds ATP synthase on the surface of human endot...	KEEP AS NON CORE	Summary: IDA annotation for CC from the angiostatin study. Direct experimental evidence for plasma membrane localization by flow cytometry and immunofluorescence. Reason: Correct. The study provided direct evidence for cell surface/plasma membrane localization using flow cytometry and immunofluorescence. This is the ecto-ATP synthase localization, secondary to mitochondrial localization. Supporting Evidence: PMID:10077593 The presence of this protein on the cell surface was confirmed by flow cytometry and immunofluorescence analysis.
GO:0005515 protein binding	IPI PMID:10077593 Angiostatin binds ATP synthase on the surface of human endot...	MARK AS OVER ANNOTATED	Summary: IPI protein binding from the angiostatin study. The study demonstrated specific binding of angiostatin to the alpha/beta subunits of ATP synthase on the cell surface, and confirmed binding to recombinant alpha subunit. Reason: The interaction with angiostatin is specific and well-characterized. However, generic "protein binding" is uninformative. The more specific GO:0043532 (angiostatin binding) is already annotated for this gene, making this generic annotation redundant. Supporting Evidence: PMID:10077593 Angiostatin also bound to the recombinant alpha-subunit of human ATP synthase, and this binding was not inhibited by a 2,500-fold molar excess of plasminogen.

Core Functions

ATP5F1A is the non-catalytic alpha subunit of the F1 head of mitochondrial ATP synthase (Complex V). Three alpha subunits alternate with three beta subunits to form the alpha3-beta3 hexameric F1 catalytic head on the matrix side of the inner mitochondrial membrane. The alpha subunit binds ATP and ADP at non-catalytic regulatory sites that are essential for the rotational binding-change mechanism, but does NOT itself catalyze ATP synthesis -- the catalytic sites reside on the beta subunit (ATP5F1B). ATP5F1A therefore contributes_to the complex-level proton-transporting ATP synthase activity (GO:0046933) but does not independently enable it. The alpha subunit also plays a structural role in maintaining the integrity of the F1 head and accommodating the symmetry mismatch between the three-fold F1 and the c-ring rotor. Pathogenic variants (R207H, R329C, Y321C) cause severe Complex V deficiency (MC5DN4A/B). Cryo-EM structures at 2.4-2.9 A resolution (PMID:37244256) reveal three alpha chains (A/B/C) alternating with three beta chains (D/E/F), with clinically relevant mutations mapping to subunit interfaces. ATP synthase assembles through two intermediates: the F1-c-ring and the b-e-g stator complex (PMID:26297831). ATP5F1A also participates in ecto-ATP synthase activity on the cell surface, where it interacts with angiostatin (PMID:10077593), HRG (PMID:19285951), and EMAP II (PMID:11741979), but this is a non-core function.

Molecular Function:

ATP binding

Directly Involved In:

proton motive force-driven mitochondrial ATP synthesis

Cellular Locations:

mitochondrial matrix

In Complex:

proton-transporting ATP synthase complex

Supporting Evidence:

PMID:37244256
Alpha subunit (chains A/B/C) alternates with beta subunit (chains D/E/F) in the F1 head. Structures reveal ADP release mechanism, symmetry mismatch accommodation, and water molecules in proton channels. Clinically relevant mutations mapped to subunit interfaces.
PMID:26297831
ATP synthase assembles through two intermediates: F1-c-ring (containing alpha, beta, and other catalytic subunits with the central rotor) and the b-e-g stator complex.
PMID:12110673
The captured complex V displayed ATP hydrolysis activity that was fully oligomycin and inhibitor protein IF(1)-sensitive

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:10077593

Angiostatin binds ATP synthase on the surface of human endothelial cells.

ATP5F1A identified as the angiostatin binding protein on endothelial cell surface by N-terminal sequencing, peptide mass fingerprinting, and immunologic analyses. Angiostatin bound recombinant alpha subunit with binding not inhibited by plasminogen. Anti-alpha-subunit antibody blocked angiostatin's antiproliferative effect by 90%.

"The presence of this protein on the cell surface was confirmed by flow cytometry and immunofluorescence analysis."

PMID:11410595

Atp11p and Atp12p are assembly factors for the F(1)-ATPase in human mitochondria.

ATPAF2 (Atp12p) is an assembly factor for the F1 component, interacting with the alpha subunit to facilitate F1 assembly.

"Atp11p and Atp12p were first described as proteins required for assembly of the F(1) component of the mitochondrial ATP synthase in Saccharomyces cerevisiae"

PMID:11741979

Interaction of the C-terminal domain of p43 and the alpha subunit of ATP synthase. Its functional implication in endothelial cell proliferation.

EMAP II binds the alpha subunit of ATP synthase on the cell surface. The interaction inhibits endothelial cell proliferation. Soluble alpha-ATP synthase relieves the antiproliferative effect.

"The isolated protein was determined to be the alpha subunit of ATP synthase. The interaction of EMAP II and alpha-ATP synthase was confirmed by enzyme-linked immunosorbent assay and in vitro pull down assays"

PMID:12110673

A functionally active human F1F0 ATPase can be purified by immunocapture from heart tissue and fibroblast cell lines. Subunit structure and activity studies.

F1F0 ATP synthase immunocaptured from human heart tissue and fibroblasts contained a full complement of subunits including alpha, beta, OSCP, d, and IF1. The captured complex displayed oligomycin-sensitive and IF1-sensitive ATP hydrolysis activity.

"The immunoprecipitated F(1)F(0) contained a full complement of subunits that were identified with specific antibodies against five of the subunits (alpha, beta, OSCP, d, and IF(1))"

PMID:15161933

Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding proteins.

PMID:15324660

Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization.

PMID:17643490

Ecto-F1-ATPase and MHC-class I close association on cell membranes.

Ecto-F1-ATPase (including alpha and beta chains) co-immunoprecipitates and co-localizes with MHC class I molecules in punctate membrane domains. Ecto-F1-ATPase epitope detection inversely correlates with MHC-I expression level.

"biotinylated F1-ATPase cell surface components co-immunoprecipitate with MHC-I molecules confirming the association of both complexes on Raji cells."

PMID:1830491

Nucleotide sequence of a cDNA for the alpha subunit of human mitochondrial ATP synthase.

Original cDNA cloning of the human ATP5F1A gene. Encoded polypeptide of 553 residues highly homologous to ATP synthase alpha subunit from other species.

"A full length cDNA clone of the alpha subunit of mitochondrial ATP synthase (EC 3.6.1.34) has been isolated"

PMID:19016746

Identification of mitochondrial F(1)F(0)-ATP synthase interacting with galectin-3 in colon cancer cells.

Galectin-3 co-localizes with ATP synthase in the inner membrane vesicles of mitochondria and has an inhibitory activity against ATP synthase.

"Galectin-3 and ATP synthase were co-isolated in the inner membrane vesicles of mitochondria."

PMID:19056867

Large-scale proteomics and phosphoproteomics of urinary exosomes.

PMID:19285951

High affinity interaction between histidine-rich glycoprotein and the cell surface type ATP synthase on T-cells.

HRG binds the alpha subunit of ATP synthase on the surface of T-cells with K_D of 66 nM. The HRG/Con A-induced morphological changes of MOLT-4 cells were specifically inhibited by anti-beta-subunit antibody.

"HRG specifically interacted with mitochondrial ATP synthase with a dissociation constant of 66 nM."

PMID:19343720

Identification and characterization of proteins interacting with SIRT1 and SIRT3: implications in the anti-aging and metabolic effects of sirtuins.

PMID:19688755

LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes.

PMID:19946888

Defining the membrane proteome of NK cells.

PMID:20618440

Proteomic and biochemical analysis of 14-3-3-binding proteins during C2-ceramide-induced apoptosis.

PMID:20833797

Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphorylation of inner membrane protein complexes and enzymes.

PMID:21106936

Regenerative protein thymosin beta-4 is a novel regulator of purinergic signaling.

Thymosin beta-4 binds the beta subunit of ecto-ATP synthase (K_D 12 nM) and increases cell surface ATP levels. Blocking antibodies and antagonists (oligomycin, piceatannol, angiostatin) inhibited the effect. P2X4 receptor mediates downstream migration.

"we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin"

PMID:22309213

Identification of a molecular component of the mitochondrial acetyltransferase programme: a novel role for GCN5L1.

GCN5L1 (BLOC1S1) is a mitochondrial acetyltransferase that interacts with and promotes acetylation of SIRT3 respiratory chain targets including ATP5F1A. GCN5L1 reverses global SIRT3 effects on mitochondrial protein acetylation.

"GCN5L1 interacts with and promotes acetylation of SIRT3 respiratory chain targets and reverses global SIRT3 effects on mitochondrial protein acetylation, respiration and bioenergetics."

PMID:22658674

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.

PMID:23533145

In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.

PMID:26297831

Assembly of human mitochondrial ATP synthase through two separate intermediates, F1-c-ring and b-e-g complex.

ATP synthase assembles through two intermediates: F1-c-ring (containing alpha, beta, and other catalytic subunits with the central rotor) and the b-e-g stator complex. The central rotor shaft and stator stalk form separately and assemble later.

"Assembly of human mitochondrial ATP synthase through two separate intermediates, F1-c-ring and b-e-g complex."

PMID:27499296

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function.

PMID:28514442

Architecture of the human interactome defines protein communities and disease networks.

PMID:30021884

Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.

PMID:33961781

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.

PMID:34800366

Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.

PMID:37244256

Structure of the human ATP synthase.

Cryo-EM structures of human ATP synthase in three main rotational states and one substate. Alpha subunit (chains A/B/C) alternates with beta subunit (chains D/E/F) in the F1 head. Structures reveal ADP release mechanism, symmetry mismatch accommodation, and water molecules in proton channels. Clinically relevant mutations mapped to subunit interfaces.

"Structure of the human ATP synthase."

file:human/ATP5F1A/ATP5F1A-deep-research-falcon.md

Falcon deep research synthesis for ATP5F1A

Deep research synthesis confirms ATP5F1A as the alpha subunit of human Complex V.

"ATP5F1A encodes the alpha subunit of the mitochondrial F1 sector of F1FO-ATP synthase (Complex V) in Homo sapiens"

PMID:40205054

Multimodal cell maps as a foundation for structural and functional genomics.

Reactome:R-HSA-164832

ATPase synthesizes ATP

Reactome:R-HSA-164834

Enzyme-bound ATP is released

Reactome:R-HSA-164840

ADP and Pi bind to ATPase

Reactome:R-HSA-8949580

F1Fo ATP synthase dimerizes

Reactome:R-HSA-9838035

CLPXP binds mitochondrial matrix proteins

Reactome:R-HSA-9838081

LONP1 degrades mitochondrial matrix proteins

Reactome:R-HSA-9838093

LONP1 binds mitochondrial matrix proteins

Reactome:R-HSA-9838289

CLPXP degrades mitochondrial matrix proteins

Reactome:R-HSA-9839105

AFG3L2 degrades mitochondrial matrix proteins

Reactome:R-HSA-9839149

AFG3L2 binds mitochondrial matrix proteins

Deep Research

Falcon

(ATP5F1A-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 14 citations 2026-02-11T08:56:05.688676

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Plan
We verified the gene/protein identity (ATP5F1A; UniProt P25705), gathered recent literature (emphasizing 2023–2024 primary research and reviews) on ATP synthase structure, regulation, disease links, and translational applications, extracted mechanistic and localization details, and synthesized findings into a concise, fully cited research report. A summary artifact is embedded to aid quick reference.

Topic	Key points (1-2 sentences)	Primary recent sources (journal, year)	URL (if available)
Identity/Verification	ATP5F1A encodes the nuclear-encoded mitochondrial F1 ATP synthase alpha subunit (part of the alpha/beta family) and corresponds to UniProt P25705.	Chouhan et al., Autophagy 2023 (Chouhan et al., 2023) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4); Lerouley et al., bioRxiv 2024 (lerouley2024novelif1mechanism pages 1-4)	https://doi.org/10.1080/15548627.2022.2103961; https://doi.org/10.1101/2024.08.06.606758
Cellular localization	Localizes to the mitochondrial matrix-facing F1 sector of the inner mitochondrial membrane and associates with the FO peripheral stalk; F1 is matrix-exposed while FO spans the membrane.	Lauterboeck et al., Cells 2024 (lauterboeck2024if1promotescellular pages 17-18); Grandi et al., IJMS 2024 (grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17)	https://doi.org/10.3390/cells13060551; https://doi.org/10.3390/ijms25094655
Core biochemical function	Functions in oxidative phosphorylation: the F1 sector synthesizes ATP from ADP + Pi driven by FO-mediated proton flow; the alpha subunit provides nucleotide-binding/noncatalytic sites and structural support in the catalytic hexamer.	Lerouley et al., bioRxiv 2024 (lerouley2024novelif1mechanism pages 1-4); Chouhan et al., Autophagy 2023 (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4)	https://doi.org/10.1101/2024.08.06.606758; https://doi.org/10.1080/15548627.2022.2103961
Catalytic mechanism & structural interfaces	ATP synthase operates by the binding-change rotary mechanism in an alpha3beta3 hexamer; alpha subunits form noncatalytic ATP-binding sites and interface with the central stalk (gamma/epsilon) and peripheral/stator subunits (OSCP/delta).	Lerouley et al., bioRxiv 2024 (lerouley2024novelif1mechanism pages 1-4); Chouhan et al., Autophagy 2023 (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4)	https://doi.org/10.1101/2024.08.06.606758; https://doi.org/10.1080/15548627.2022.2103961
Regulation (IF1/OSCP, phosphorylation incl. TNK2)	Endogenous inhibitor IF1 binds F1/OSCP to block ATP hydrolysis (pH- and phosphorylation-regulated); TNK2/ACK1 phosphorylates ATP5F1A (Y243/Y246) to increase complex stability/activity in cancer, reducing IF1 binding.	Koníčková 2024 (review) (konickova2024patofyziologickédopadyporuch pages 32-34); Chouhan et al., Autophagy 2023 (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4); Grandi et al., IJMS 2024 (grandi2024peptidestargetingthe pages 16-17)	https://doi.org/10.1101/2024.08.06.606758; https://doi.org/10.1080/15548627.2022.2103961; https://doi.org/10.3390/ijms25094655
Higher-order organization (dimers/tetramers)	ATP synthase forms dimers/oligomers that shape cristae; recent cryo-EM work documents mammalian dimer/tetramer assemblies and IF1-associated oligomeric states.	Grandi et al., IJMS 2024 (grandi2024peptidestargetingthe pages 16-17); Lauterboeck et al., Cells 2024 (lauterboeck2024if1promotescellular pages 17-18)	https://doi.org/10.3390/ijms25094655; https://doi.org/10.3390/cells13060551
Human disease links (general)	Defects in complex V assembly/subunits cause mitochondrial disorders (encephalopathies, cardiomyopathies); assembly-factor and subunit dysfunctions are implicated though specific ATP5F1A variant counts were not retrieved here.	Koníčková 2024 (review) (konickova2024patofyziologickédopadyporuch pages 32-34); Lerouley et al., bioRxiv 2024 (lerouley2024novelif1mechanism pages 1-4)	https://doi.org/10.1101/2024.08.06.606758
Cancer / biomarker relevance	ATP5F1A activity/expression and its phosphorylation (p‑Y-ATP5F1A) associate with cancer cell survival and represent potential biomarkers/vulnerabilities (e.g., prostate cancer TNK2 axis).	Chouhan et al., Autophagy 2023 (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4); Grandi et al., IJMS 2024 (grandi2024peptidestargetingthe pages 15-16)	https://doi.org/10.1080/15548627.2022.2103961; https://doi.org/10.3390/ijms25094655
Therapeutic / experimental applications	Experimental peptides that displace IF1 from OSCP modulate permeability transition and apoptosis in cancer cells; TNK2 inhibitors (targeting p‑Y‑ATP5F1A) produce mitophagy-based anti-tumor effects in models.	Grandi et al., IJMS 2024 (grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17); Chouhan et al., Autophagy 2023 (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4)	https://doi.org/10.3390/ijms25094655; https://doi.org/10.1080/15548627.2022.2103961
Notable 2023–2024 advances	Key recent advances: TNK2/ACK1 phosphorylation of ATP5F1A (Autophagy 2023) and 2024 studies refining IF1 mechanism and peptide displacement of IF1 (bioRxiv 2024; IJMS 2024), advancing regulatory and translational targeting knowledge.	Chouhan et al., Autophagy 2023 (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4); Lerouley et al., bioRxiv 2024 (lerouley2024novelif1mechanism pages 1-4); Grandi et al., IJMS 2024 (grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17)	https://doi.org/10.1080/15548627.2022.2103961; https://doi.org/10.1101/2024.08.06.606758; https://doi.org/10.3390/ijms25094655

Table: A concise evidence-backed table summarizing ATP5F1A (UniProt P25705): identity, function, localization, regulation, disease relevance and recent (2023–2024) findings with primary sources cited for follow-up.

Comprehensive research report: ATP5F1A (UniProt P25705)

1) Key concepts and definitions with current understanding
- Identity and nomenclature. ATP5F1A encodes the alpha subunit of the mitochondrial F1 sector of F1FO-ATP synthase (Complex V) in Homo sapiens; it is a member of the conserved F-type ATPase alpha/beta chains family. The alpha subunit forms part of the catalytic head (F1) and provides noncatalytic nucleotide-binding sites within the α3β3 hexamer (the β subunits host the catalytic sites). This aligns with the UniProt description for P25705 and with structural/mechanistic literature on mammalian ATP synthase (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4). Mechanistic reviews and experimental work describe the F1 composition as α3β3γδε, consistent with ATP5F1A’s role in the α3β3 head (bioRxiv, Dec 2024; URL: https://doi.org/10.1101/2024.08.06.606758) (lerouley2024novelif1mechanism pages 1-4).
- Cellular localization. ATP5F1A resides in the mitochondrial matrix-facing F1 domain that is attached to the inner mitochondrial membrane-embedded FO sector; thus its functional location is the matrix side of the inner membrane (Cells, Mar 2024; URL: https://doi.org/10.3390/cells13060551; IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17).
- Core biochemical function. Within F1FO-ATP synthase, chemiosmotic proton flow through FO drives rotation of the central stalk and conformational cycling in α/β pairs (binding-change mechanism) to synthesize ATP from ADP and Pi; the alpha subunits contribute noncatalytic nucleotide-binding and structural roles essential for the β-subunit catalytic chemistry (bioRxiv, Dec 2024; URL: https://doi.org/10.1101/2024.08.06.606758; Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (lerouley2024novelif1mechanism pages 1-4, chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).

2) Recent developments and latest research (prioritize 2023–2024)
- Human cancer signaling to ATP5F1A via tyrosine phosphorylation. A 2023 study showed the non-receptor tyrosine kinase TNK2/ACK1 phosphorylates ATP5F1A at Y243/Y246 (mature protein Y200/Y203), stabilizes complex V, augments mitochondrial energy output, and diminishes binding to the physiological inhibitor ATPIF1; TNK2 inhibition reverses these effects and induces mitophagy-based tumor suppression in prostate cancer models (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).
- IF1 (ATPIF1) regulation and mechanism refinements. 2024 work and curated reviews emphasize that IF1 binds the F1/OSCP region of ATP synthase to block ATP hydrolysis in a pH-regulated manner, with mitochondrial PKA-dependent phosphorylation of IF1 preventing its inhibitory binding; recent cellular studies further highlight IF1’s roles in bioenergetics, oligomerization, and stress adaptation (review/overview sources compiled within 2024 texts) (bioRxiv, Dec 2024; URL: https://doi.org/10.1101/2024.08.06.606758; Cells, Mar 2024; URL: https://doi.org/10.3390/cells13060551; IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655; 2024 review highlighting PKA modulation cited therein) (lerouley2024novelif1mechanism pages 1-4, lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 15-16, konickova2024patofyziologickédopadyporuch pages 32-34).
- Therapeutic peptide strategies targeting the IF1–OSCP interface. In 2024, mitochondria-targeting peptides designed to displace IF1 from OSCP modulated the mitochondrial permeability transition in HeLa cells and altered apoptosis susceptibility without impairing respiration, suggesting tractable modulation of ATP synthase–IF1 interactions for therapy (IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17).
- Structural advances. Recent cryo-EM studies (2019–2020 and further summarized in 2024 articles) revealed mammalian ATP synthase dimer/tetramer assemblies and IF1-bound states, reinforcing current models of α3β3 head architecture and peripheral/central stalk interfaces, which define ATP5F1A’s positioning in the complex (Cells, Mar 2024; URL: https://doi.org/10.3390/cells13060551; IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 16-17).

3) Current applications and real-world implementations
- Oncology applications. The TNK2–ATP5F1A phosphorylation axis identifies a mitochondrial bioenergetic dependency in prostate cancer, with a small-molecule TNK2 inhibitor ((R)-9b) triggering cancer-selective mitophagy; phosphorylation state (p-Y-ATP5F1A) emerges as a potential biomarker and pharmacodynamic readout (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).
- Peptide modulators of IF1–OSCP. Mitochondria-targeted peptides that interfere with IF1–OSCP binding can tune mitochondrial permeability transition/apoptosis in cancer cells, pointing to prototype therapeutics modulating ATP synthase regulation rather than the catalytic core (IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17).

4) Expert opinions and analysis from authoritative sources
- Mechanistic consensus. Contemporary structural/mechanistic syntheses reaffirm the binding-change/rotary catalysis mechanism, the α3β3 architecture, and the matrix-exposed localization of F1, placing ATP5F1A in noncatalytic yet essential nucleotide-binding/structural roles that coordinate with β catalytic sites and central/peripheral stalks (bioRxiv, Dec 2024; URL: https://doi.org/10.1101/2024.08.06.606758; Cells, Mar 2024; URL: https://doi.org/10.3390/cells13060551) (lerouley2024novelif1mechanism pages 1-4, lauterboeck2024if1promotescellular pages 17-18).
- Regulation by IF1 and phosphorylation pathways. Reviews and recent experiments converge on IF1 as a physiological, pH- and phosphorylation-regulated brake on ATP hydrolysis that can influence cristae organization and stress adaptation. Phosphorylation pathways that modify ATP5F1A itself (TNK2) or IF1 (PKA) exemplify how signaling impinges on OXPHOS output and mitochondrial resilience in disease contexts including cancer (review references collated within 2024 sources; Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (konickova2024patofyziologickédopadyporuch pages 32-34, chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4, lauterboeck2024if1promotescellular pages 17-18).

5) Relevant statistics and data from recent studies
- Site-specific phosphorylation of ATP5F1A. TNK2 directly phosphorylates ATP5F1A at Y243/Y246; phospho-specific antibodies and mutational analyses (Y243/246A) demonstrate reduced basal OCR and membrane potential when phosphorylation is prevented, quantitatively linking p-Y-ATP5F1A to increased respiratory capacity in prostate cancer cells (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).
- Modulation of permeability transition by IF1–OSCP peptides. In situ peptide treatments in HeLa cells altered mitochondrial permeability transition metrics without depressing respiration, separating apoptotic control from ATP production and supporting a feasible therapeutic window (IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (grandi2024peptidestargetingthe pages 15-16).

Detailed mechanistic role of ATP5F1A within F1FO-ATP synthase
- Catalytic role and substrate specificity. The enzyme ATP synthase catalyzes ADP + Pi → ATP; catalysis occurs at β subunits, whereas α subunits (ATP5F1A) provide noncatalytic nucleotide-binding sites and structural scaffolding necessary for binding-change transitions and torque coupling from the central stalk (bioRxiv, Dec 2024; URL: https://doi.org/10.1101/2024.08.06.606758) (lerouley2024novelif1mechanism pages 1-4).
- Structural interfaces. ATP5F1A subunits alternate with β around the central stalk (γ/ε), contact the peripheral stator via δ/OSCP, and participate in the α/β head that couples to the FO rotor/stator; these interfaces are supported by mammalian cryo-EM organizations including IF1-bound states (Cells, Mar 2024; URL: https://doi.org/10.3390/cells13060551; IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 16-17).
- Localization. ATP5F1A operates in the mitochondrial matrix-facing F1 domain attached to the inner mitochondrial membrane (lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17).

Regulation of ATP5F1A/ATP synthase
- Endogenous inhibitor IF1/ATPIF1. IF1 binds the F1/OSCP region to prevent wasteful ATP hydrolysis in the reverse mode; its inhibitory effect is pH-dependent and attenuated by PKA-mediated phosphorylation of IF1, releasing ATP synthase activity (bioRxiv, Dec 2024; URL: https://doi.org/10.1101/2024.08.06.606758; review citations compiled there; IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (lerouley2024novelif1mechanism pages 1-4, konickova2024patofyziologickédopadyporuch pages 32-34, grandi2024peptidestargetingthe pages 16-17).
- Oncogenic kinase regulation. TNK2/ACK1 phosphorylation of ATP5F1A increases complex V stability and mitochondrial energy output while reducing ATPIF1 binding; TNK2 inhibition ((R)-9b) reverses these effects and induces mitophagy with anti-tumor consequences in prostate cancer models (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).

Higher-order organization and functional implications
- Dimers/oligomers and cristae. Mammalian ATP synthase forms dimers and higher oligomers that sculpt cristae; IF1-bound states and peripheral stalk/OSCP interactions influence oligomerization and stress responses, reinforcing the architectural context for ATP5F1A function (Cells, Mar 2024; URL: https://doi.org/10.3390/cells13060551; IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 16-17).

Human disease associations
- Mitochondrial disease (general). Reviews summarizing complex V defects link ATP synthase subunits/assembly factors to encephalopathy, cardiomyopathy, and Leigh-like syndromes; while gene-by-gene statistics for ATP5F1A variants were not retrieved here, the disease literature situates ATP5F1A within essential Complex V function where subunit dysfunction is pathologic (review overview 2024 with human disease references) (konickova2024patofyziologickédopadyporuch pages 32-34).
- Cancer. Phosphorylation of ATP5F1A by TNK2 supports prostate cancer cell survival and bioenergetics; inhibiting this axis yields mitophagy-based tumor control, highlighting p‑Y‑ATP5F1A as a candidate biomarker/vulnerability (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).

Real-world implementations and translational potential
- Pharmacologic kinase targeting. TNK2 inhibitors (e.g., (R)-9b) are leveraged to collapse the ATP5F1A phosphorylation-dependent energy gain and trigger mitophagy in tumors, suggesting a “mitocan” strategy targeting OXPHOS regulation (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).
- Peptide-based modulators. Cell-permeable peptides aimed at the IF1–OSCP interface provide proof-of-concept for modulating apoptosis via ATP synthase regulatory contacts without impairing respiratory flux, with implications for anti-cancer therapy development (IJMS, Apr 2024; URL: https://doi.org/10.3390/ijms25094655) (grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17).

Mandatory verification
- Gene symbol/protein description match. ATP5F1A encodes the mitochondrial ATP synthase F1 alpha subunit in human; the literature above directly uses “ATP5F1A (ATP synthase F1 subunit alpha)” and places it in the F1 catalytic head, matching the UniProt-provided description (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).
- Organism. All functional/structural claims cited here pertain to mammalian/human ATP synthase or human cancer models, satisfying Homo sapiens relevance (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4, lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17).
- Family/domains alignment. Sources consistently describe ATP5F1A as the F-type ATPase alpha subunit in the α/β family, embedded in the α3β3 head of F1, agreeing with the ATPase alpha/beta chain family/domain annotations (Autophagy, Jul 2023; URL: https://doi.org/10.1080/15548627.2022.2103961; bioRxiv, Dec 2024; URL: https://doi.org/10.1101/2024.08.06.606758) (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4, lerouley2024novelif1mechanism pages 1-4).
- Ambiguity check. No conflicting gene symbol usage was found within the cited human-focused sources; references clearly denote ATP5F1A as the mitochondrial F1 alpha subunit in human contexts (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4, lauterboeck2024if1promotescellular pages 17-18).

Limitations and data gaps
- Specific human genetics statistics (e.g., counts of pathogenic ATP5F1A variants, prevalence) and comprehensive 2023–2024 expression-dataset meta-analyses were not retrieved in the gathered evidence. The disease connections summarized above reflect authoritative overviews rather than ATP5F1A-variant case series; targeted genetics resources would be needed for variant-level statistics (konickova2024patofyziologickédopadyporuch pages 32-34).

References with URLs and dates
- Chouhan S. et al. TNK2/ACK1-mediated phosphorylation of ATP5F1A augments prostate cancer survival and creates mitochondrial vulnerability. Autophagy. Jul 2023. URL: https://doi.org/10.1080/15548627.2022.2103961 (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4).
- Lerouley O. et al. Novel IF1 mechanism preventing ATP hydrolysis by the ATP synthase subcomplex in S. cerevisiae (conserved regulatory insights). bioRxiv. Dec 2024. URL: https://doi.org/10.1101/2024.08.06.606758 (lerouley2024novelif1mechanism pages 1-4, lerouley2024novelif1mechanism pages 30-32, lerouley2024novelif1mechanism pages 32-33).
- Grandi M. et al. Peptides targeting the IF1–ATP synthase complex modulate the permeability transition pore in cancer HeLa cells. Int J Mol Sci. Apr 2024. URL: https://doi.org/10.3390/ijms25094655 (grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17).
- Lauterboeck L. et al. IF1 promotes cellular proliferation and inhibits oxidative phosphorylation in mouse embryonic fibroblasts. Cells. Mar 2024. URL: https://doi.org/10.3390/cells13060551 (lauterboeck2024if1promotescellular pages 17-18).
- Koníčková S. Patofyziologické dopady poruch mitochondriální F1FO ATP syntázy (review summarizing Complex V disease and regulation). 2024. (Context cites IF1 regulation and Complex V disease literature) (konickova2024patofyziologickédopadyporuch pages 32-34).

Conclusion
ATP5F1A (P25705) is the human mitochondrial F1 alpha subunit, essential for the α3β3 catalytic head that executes binding-change catalysis; it localizes to the matrix-exposed F1 domain of the inner mitochondrial membrane. Recent work illuminates regulatory control by IF1 and oncogenic signaling via TNK2 phosphorylation of ATP5F1A, with translational avenues emerging from kinase inhibitors and peptides that modulate the IF1–OSCP interface. While comprehensive 2023–2024 variant statistics were not captured here, the assembled evidence underscores ATP5F1A’s central biochemical role, regulatory interactions, and growing clinical relevance in cancer bioenergetics and mitochondrial stress responses (chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4, lerouley2024novelif1mechanism pages 1-4, lauterboeck2024if1promotescellular pages 17-18, grandi2024peptidestargetingthe pages 15-16, grandi2024peptidestargetingthe pages 16-17, konickova2024patofyziologickédopadyporuch pages 32-34).

References

(chouhan2023tnk2ack1mediatedphosphorylationof pages 2-4): Surbhi Chouhan, Mithila Sawant, Cody Weimholt, Jingqin Luo, Robert W. Sprung, Mailyn Terrado, David M. Mueller, H. Shelton Earp, and Nupam P. Mahajan. Tnk2/ack1-mediated phosphorylation of atp5f1a (atp synthase f1 subunit alpha) selectively augments survival of prostate cancer while engendering mitochondrial vulnerability. Autophagy, 19:1000-1025, Jul 2023. URL: https://doi.org/10.1080/15548627.2022.2103961, doi:10.1080/15548627.2022.2103961. This article has 47 citations and is from a domain leading peer-reviewed journal.
(lerouley2024novelif1mechanism pages 1-4): Orane Lerouley, Isabelle Larrieu, Tom Louis Ducrocq, Benoît Pinson, Marie-France Giraud, and Arnaud Mourier. Novel if1 mechanism preventing atp hydrolysis by the atp synthase subcomplex in saccharomyces cerevisiae. bioRxiv, Dec 2024. URL: https://doi.org/10.1101/2024.08.06.606758, doi:10.1101/2024.08.06.606758. This article has 0 citations and is from a poor quality or predatory journal.
(lauterboeck2024if1promotescellular pages 17-18): Lothar Lauterboeck, Sung Wook Kang, Donnell White, Rong Bao, Parnia Mobasheran, and Qinglin Yang. If1 promotes cellular proliferation and inhibits oxidative phosphorylation in mouse embryonic fibroblasts under normoxia and hypoxia. Cells, 13:551, Mar 2024. URL: https://doi.org/10.3390/cells13060551, doi:10.3390/cells13060551. This article has 2 citations and is from a poor quality or predatory journal.
(grandi2024peptidestargetingthe pages 15-16): Martina Grandi, Simone Fabbian, Giancarlo Solaini, Alessandra Baracca, Massimo Bellanda, and Valentina Giorgio. Peptides targeting the if1–atp synthase complex modulate the permeability transition pore in cancer hela cells. International Journal of Molecular Sciences, 25:4655, Apr 2024. URL: https://doi.org/10.3390/ijms25094655, doi:10.3390/ijms25094655. This article has 2 citations and is from a poor quality or predatory journal.
(grandi2024peptidestargetingthe pages 16-17): Martina Grandi, Simone Fabbian, Giancarlo Solaini, Alessandra Baracca, Massimo Bellanda, and Valentina Giorgio. Peptides targeting the if1–atp synthase complex modulate the permeability transition pore in cancer hela cells. International Journal of Molecular Sciences, 25:4655, Apr 2024. URL: https://doi.org/10.3390/ijms25094655, doi:10.3390/ijms25094655. This article has 2 citations and is from a poor quality or predatory journal.
(konickova2024patofyziologickédopadyporuch pages 32-34): S Koníčková. Patofyziologické dopady poruch mitochondriální f1fo atp syntázy. Unknown journal, 2024.
(lerouley2024novelif1mechanism pages 30-32): Orane Lerouley, Isabelle Larrieu, Tom Louis Ducrocq, Benoît Pinson, Marie-France Giraud, and Arnaud Mourier. Novel if1 mechanism preventing atp hydrolysis by the atp synthase subcomplex in saccharomyces cerevisiae. bioRxiv, Dec 2024. URL: https://doi.org/10.1101/2024.08.06.606758, doi:10.1101/2024.08.06.606758. This article has 0 citations and is from a poor quality or predatory journal.
(lerouley2024novelif1mechanism pages 32-33): Orane Lerouley, Isabelle Larrieu, Tom Louis Ducrocq, Benoît Pinson, Marie-France Giraud, and Arnaud Mourier. Novel if1 mechanism preventing atp hydrolysis by the atp synthase subcomplex in saccharomyces cerevisiae. bioRxiv, Dec 2024. URL: https://doi.org/10.1101/2024.08.06.606758, doi:10.1101/2024.08.06.606758. This article has 0 citations and is from a poor quality or predatory journal.

Citations

grandi2024peptidestargetingthe pages 16-17
grandi2024peptidestargetingthe pages 15-16
https://doi.org/10.1080/15548627.2022.2103961;
https://doi.org/10.1101/2024.08.06.606758
https://doi.org/10.3390/cells13060551;
https://doi.org/10.3390/ijms25094655
https://doi.org/10.1101/2024.08.06.606758;
https://doi.org/10.1080/15548627.2022.2103961
https://doi.org/10.3390/ijms25094655;
https://doi.org/10.3390/cells13060551
https://doi.org/10.1080/15548627.2022.2103961,
https://doi.org/10.1101/2024.08.06.606758,
https://doi.org/10.3390/cells13060551,
https://doi.org/10.3390/ijms25094655,

📄 View Raw YAML

id: P25705
gene_symbol: ATP5F1A
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  ATP5F1A encodes the alpha subunit of the mitochondrial F1Fo-ATP synthase (Complex
  V).
  Three copies of the alpha subunit alternate with three beta subunits (ATP5F1B) to
  form the
  alpha3-beta3 hexameric F1 catalytic head, which faces the mitochondrial matrix.
  Crucially,
  the alpha subunit provides the NON-CATALYTIC nucleotide-binding sites; catalytic
  ATP synthesis
  occurs at the beta subunit active sites (PMID:37244256). The alpha subunit plays
  a structural
  and regulatory role, binding ATP and ADP at non-catalytic sites that are essential
  for the
  binding-change rotary mechanism but do not directly catalyze ATP formation. Cryo-EM
  structures
  confirm that ATP5F1A forms a homotrimer that alternates with the beta subunit trimer
  around the
  central gamma subunit stalk (PMID:37244256). ATP5F1A is also present on the cell
  surface as
  part of ecto-ATP synthase, where it functions as a receptor for angiostatin (PMID:10077593),
  histidine-rich glycoprotein (PMID:19285951), and EMAP II/p43 (PMID:11741979), with
  roles
  in angiogenesis regulation. Pathogenic variants cause mitochondrial complex V deficiency
  (MC5DN4A, MC5DN4B, COXPD22). UniProt states that the alpha subunit "does not bear
  the
  catalytic high-affinity ATP-binding sites" (P25705).
alternative_products:
- name: '1'
  id: P25705-1
- name: '2'
  id: P25705-2
  sequence_note: VSP_045129
- name: '3'
  id: P25705-3
  sequence_note: VSP_054688
existing_annotations:
# ============================================================
# IBA ANNOTATIONS (Phylogenetic inference - generally reliable)
# ============================================================
- term:
    id: GO:0045259
    label: proton-transporting ATP synthase complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for CC. ATP5F1A is a core structural component of the proton-transporting
      ATP synthase complex (Complex V). This is well supported by cryo-EM structural
      data
      (PMID:37244256), immunocapture studies (PMID:12110673), and assembly studies
      (PMID:26297831).
    action: ACCEPT
    reason: >-
      This is the defining complex membership for ATP5F1A. The alpha subunit is
      one
      of the major
      subunits of the F1 catalytic head. Cryo-EM structures show ATP5F1A as chains
      A/B/C in the
      alpha3-beta3 hexamer (PMID:37244256). IBA annotation is appropriate and well
      conserved across
      the ATPase alpha/beta chains family.
    additional_reference_ids:
    - file:human/ATP5F1A/ATP5F1A-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        Biological energy currency ATP is produced by F1Fo-ATP synthase. However,
        the molecular
        mechanism for human ATP synthase action remains unknown. Here, we present
        snapshot images
        for three main rotational states and one substate of human ATP synthase
        using
        cryoelectron microscopy.
    - reference_id: PMID:12110673
      supporting_text: >-
        The immunoprecipitated F(1)F(0) contained a full complement of subunits
        that
        were
        identified with specific antibodies against five of the subunits (alpha,
        beta,
        OSCP,
        d, and IF(1))
    - reference_id: file:human/ATP5F1A/ATP5F1A-deep-research-falcon.md
      supporting_text: >-
        ATP5F1A encodes the alpha subunit of the mitochondrial F1 sector of
        F1FO-ATP synthase (Complex V) in Homo sapiens
- term:
    id: GO:0015986
    label: proton motive force-driven ATP synthesis
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for BP. Proton motive force-driven ATP synthesis is the core
      biological
      process in which ATP5F1A participates as part of Complex V. While the alpha
      subunit does
      not directly catalyze ATP synthesis (that occurs at the beta subunit), it
      is
      essential for
      the process through its structural and regulatory roles.
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A is an essential component of the Complex V machinery that
      carries
      out proton
      motive force-driven ATP synthesis. The alpha subunit provides non-catalytic
      nucleotide-binding
      sites that are required for the binding-change mechanism. Well supported by
      structural evidence
      (PMID:37244256) and assembly studies (PMID:26297831).
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        Biological energy currency ATP is produced by F1Fo-ATP synthase
    - reference_id: PMID:26297831
      supporting_text: >-
        Mitochondrial ATP synthase is a motor enzyme in which a central shaft
        rotates
        in
        the stator casings fixed with the peripheral stator stalk.
- term:
    id: GO:0046933
    label: proton-transporting ATP synthase activity, rotational mechanism
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: contributes_to
  review:
    summary: >-
      IBA annotation for MF with contributes_to qualifier. The alpha subunit contributes
      to the
      proton-transporting ATP synthase activity of the holoenzyme complex via the
      rotational
      mechanism. The contributes_to qualifier is essential here because ATP5F1A
      provides
      non-catalytic nucleotide-binding sites -- the catalytic sites reside on the
      beta subunit
      (ATP5F1B).
    action: ACCEPT
    reason: >-
      The contributes_to qualifier is correct and important for the alpha subunit.
      Unlike the beta
      subunit which houses the catalytic nucleotide-binding sites, the alpha subunit
      provides
      structural support and non-catalytic nucleotide binding required for the rotational
      mechanism
      but does not itself catalyze ATP synthesis. UniProt states for P25705: "Subunit
      alpha does
      not bear the catalytic high-affinity ATP-binding sites." The rotational mechanism
      requires
      the full assembled complex.
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        The accommodation of the symmetry mismatch between F1 and Fo motors is
        resolved
        by
        the torsional flexing of the entire complex, especially the gamma subunit,
        and the
        rotational substep of the c subunit.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for MF. ATP binding is well established for the alpha subunit,
      which has
      non-catalytic nucleotide-binding sites. Cryo-EM structures (PMID:37244256)
      show
      ATP bound
      at multiple positions on the alpha subunit, and UniProt documents binding
      residues
      at
      positions 215, 217-220, 473, 475 as confirmed by PDB structures 8H9V and 8KI3.
    action: ACCEPT
    reason: >-
      Correct. The alpha subunit binds ATP at its non-catalytic sites. While these
      are regulatory
      rather than catalytic binding sites, ATP binding itself is accurately annotated.
      The term
      GO:0005524 does not distinguish catalytic from non-catalytic binding, so this
      is appropriate.
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        Biological energy currency ATP is produced by F1Fo-ATP synthase. However,
        the molecular
        mechanism for human ATP synthase action remains unknown. Here, we present
        snapshot images
        for three main rotational states and one substate of human ATP synthase
- term:
    id: GO:0043531
    label: ADP binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for MF. ADP binding is a well-established function of the alpha
      subunit at
      its non-catalytic nucleotide-binding sites. The alpha subunit binds ADP and
      ATP at these
      regulatory sites as part of the binding-change mechanism.
    action: ACCEPT
    reason: >-
      Correct. The alpha subunit has non-catalytic nucleotide-binding sites that
      bind
      both ADP and
      ATP. Well supported phylogenetically and structurally.
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        These structures reveal that the release of ADP occurs when the beta subunit
        of F1Fo-ATP
        synthase is in the open conformation, showing how ADP binding is coordinated
        during
        synthesis
# ============================================================
# IEA ANNOTATIONS (Electronic annotations - check for accuracy)
# ============================================================
- term:
    id: GO:0000166
    label: nucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation for MF based on UniProtKB keyword mapping. Nucleotide binding
      is correct
      but very general for ATP5F1A, which specifically binds ATP and ADP at non-catalytic
      sites.
    action: ACCEPT
    reason: >-
      Correct but broad IEA annotation. The alpha subunit has well-characterized
      nucleotide
      (ADP/ATP) binding sites documented by cryo-EM (PMID:37244256). More specific
      terms like
      GO:0005524 (ATP binding) and GO:0043531 (ADP binding) are also present in
      the
      annotation
      set, so this broader term is acceptable as an IEA inference.
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        Biological energy currency ATP is produced by F1Fo-ATP synthase
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for MF duplicating the IBA annotation for the same GO term.
      ATP
      binding is
      well established for the alpha subunit at its non-catalytic sites.
    action: ACCEPT
    reason: >-
      Correct and consistent with the IBA annotation. Duplicate evidence codes for
      the same term
      are fine. UniProt documents ATP binding residues with structural evidence
      (PDB:
      8H9V, 8KI3).
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for CC. Mitochondrial localization is well established for
      ATP5F1A,
      which
      has a mitochondrial transit peptide (residues 1-43, UniProt).
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A is a mitochondrial protein with a confirmed transit peptide.
      Localization
      to mitochondria is supported by multiple experimental methods and databases.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for CC. ATP5F1A is a peripheral membrane protein on the matrix
      side of the
      mitochondrial inner membrane, as part of the F1 head of the ATP synthase complex.
    action: ACCEPT
    reason: >-
      Correct. UniProt states ATP5F1A localizes to "Mitochondrion inner membrane;
      Peripheral
      membrane protein; Matrix side" with evidence by similarity. The F1 head is
      attached
      to the
      inner membrane via the central and peripheral stalks.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation for CC based on UniProt subcellular location mapping. ATP5F1A
      is present
      on the plasma membrane as part of the ecto-ATP synthase complex, documented
      experimentally
      by flow cytometry and immunofluorescence (PMID:10077593).
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but represents a non-core localization. Plasma membrane localization
      relates to the
      ecto-ATP synthase function, which is secondary to the primary mitochondrial
      localization.
      Experimentally confirmed by Moser et al. who demonstrated cell surface presence
      by flow
      cytometry and immunofluorescence analysis (PMID:10077593).
    supported_by:
    - reference_id: PMID:10077593
      supporting_text: >-
        The presence of this protein on the cell surface was confirmed by flow
        cytometry
        and
        immunofluorescence analysis.
- term:
    id: GO:0006754
    label: ATP biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation for BP based on UniProt keyword mapping. ATP biosynthetic process
      is a core
      function of the ATP synthase complex to which ATP5F1A contributes as a structural
      and
      regulatory subunit.
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A is an essential component of Complex V which synthesizes
      ATP.
      While the
      catalytic activity resides in the beta subunit, the alpha subunit is required
      for the
      process. This is a broad but accurate term.
- term:
    id: GO:0006811
    label: monoatomic ion transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation for BP. This term refers to ion transport, which is related
      to
      the proton
      transport function of the ATP synthase complex but is extremely broad.
    action: ACCEPT
    reason: >-
      While very general, this is not incorrect since the F1Fo-ATP synthase complex
      transports
      protons (H+) across the inner mitochondrial membrane. ATP5F1A contributes
      to
      this function
      as part of the complex. More specific annotations for proton transport are
      also
      present.
- term:
    id: GO:0015986
    label: proton motive force-driven ATP synthesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA annotation for BP based on InterPro mapping. Duplicates the IBA annotation
      for
      the same term. Correct.
    action: ACCEPT
    reason: >-
      Correct and consistent with the IBA annotation. Proton motive force-driven
      ATP
      synthesis
      is the core biological process of Complex V. Duplicate evidence from IEA is
      acceptable.
- term:
    id: GO:0016469
    label: proton-transporting two-sector ATPase complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for CC based on ARBA machine learning model. This term describes
      the broader
      class of two-sector ATPase complexes (F-type, V-type, A-type). The mitochondrial
      ATP synthase
      is an F-type two-sector ATPase.
    action: ACCEPT
    reason: >-
      Correct but general. The F1Fo ATP synthase is indeed a proton-transporting
      two-sector
      ATPase
      complex. More specific annotations for the proton-transporting ATP synthase
      complex
      (GO:0045259) are also present. As an IEA from ARBA, the broader term is acceptable.
- term:
    id: GO:0032559
    label: adenyl ribonucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA annotation for MF based on InterPro mapping. Adenyl ribonucleotide binding
      includes
      both ATP and ADP binding, which is correct for the alpha subunit's non-catalytic
      nucleotide-binding sites.
    action: ACCEPT
    reason: >-
      Correct but broad. The alpha subunit binds adenyl ribonucleotides (ATP and
      ADP)
      at its
      non-catalytic sites. More specific terms (GO:0005524 ATP binding, GO:0043531
      ADP binding)
      are already annotated. As an IEA this broader term is acceptable.
- term:
    id: GO:0045259
    label: proton-transporting ATP synthase complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for CC, duplicating the IBA annotation for the same GO term.
      Correct.
    action: ACCEPT
    reason: >-
      Correct and consistent with the IBA annotation. Duplicate evidence codes for
      the same
      term are fine.
- term:
    id: GO:0046034
    label: ATP metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA annotation for BP based on InterPro mapping. ATP metabolic process is
      very
      broad,
      encompassing both ATP synthesis and hydrolysis.
    action: ACCEPT
    reason: >-
      Correct but very general. ATP5F1A is involved in ATP metabolism (primarily
      synthesis
      as part
      of Complex V, but the complex can also hydrolyze ATP). More specific annotations
      for ATP
      biosynthetic process and proton motive force-driven ATP synthesis are present.
- term:
    id: GO:0046933
    label: proton-transporting ATP synthase activity, rotational mechanism
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for MF, duplicating the IBA annotation for the same GO term.
      Note this IEA
      lacks the contributes_to qualifier that the IBA has, which is important for
      the alpha subunit
      since the catalytic activity resides in the beta subunit.
    action: ACCEPT
    reason: >-
      Correct term but ideally should have the contributes_to qualifier as in the
      IBA annotation.
      For the alpha subunit, which provides non-catalytic nucleotide-binding sites,
      the
      contributes_to qualifier is particularly important. However, as an IEA the
      absence
      of the
      qualifier is a minor issue.
- term:
    id: GO:1902495
    label: transmembrane transporter complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for CC based on ARBA. The ATP synthase complex is a transmembrane
      transporter
      complex that translocates protons across the membrane.
    action: ACCEPT
    reason: >-
      Correct but very general. The F1Fo-ATP synthase is indeed a transmembrane
      transporter
      complex. More specific terms (GO:0045259, GO:0016469) are also annotated.
- term:
    id: GO:1902600
    label: proton transmembrane transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for BP. Proton transmembrane transport is a core process of
      the
      ATP
      synthase complex.
    action: ACCEPT
    reason: >-
      Correct. The F1Fo-ATP synthase transports protons across the inner mitochondrial
      membrane
      as part of its catalytic cycle. ATP5F1A contributes to this as a structural
      subunit of
      the F1 head.
# ============================================================
# PROTEIN BINDING ANNOTATIONS (IPI) - Many from HTP studies
# ============================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11410595
  review:
    summary: >-
      IPI protein binding from a study demonstrating that Atp11p and Atp12p (ATPAF1/ATPAF2)
      are assembly factors for F1-ATPase in human mitochondria (Wang et al. 2001).
      UniProt
      confirms the interaction with ATPAF2 (PubMed:11410595). This is a specific,
      functionally
      characterized interaction with an assembly chaperone.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interaction with ATPAF2 is specific and functionally meaningful -- ATPAF2
      is a
      dedicated assembly factor for ATP5F1A. However, the generic "protein binding"
      term is
      uninformative. A more specific term capturing the chaperone/assembly factor
      interaction
      would be preferable, but such a term may not exist in GO.
    supported_by:
    - reference_id: PMID:11410595
      supporting_text: >-
        Atp11p and Atp12p were first described as proteins required for assembly
        of
        the F(1)
        component of the mitochondrial ATP synthase in Saccharomyces cerevisiae
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15161933
  review:
    summary: >-
      IPI protein binding from a large-scale proteomic analysis of 14-3-3-binding
      proteins
      (Meek et al. 2004). ATP5F1A was identified as a 14-3-3-binding protein in
      HeLa
      cells.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This is a high-throughput proteomic study identifying many 14-3-3-binding
      proteins.
      While
      the interaction may be real, the generic "protein binding" term is uninformative
      and the
      biological significance of 14-3-3 binding to ATP5F1A is not characterized.
    supported_by:
    - reference_id: PMID:15161933
      supporting_text: >-
        Comprehensive proteomic analysis of interphase and mitotic 14-3-3-binding
        proteins.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15324660
  review:
    summary: >-
      IPI protein binding from another 14-3-3-binding protein study (Jin et al.
      2004).
      Focused
      on cytoskeletal regulation and cellular organization.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      High-throughput 14-3-3 interaction proteomics study. Generic protein binding
      is uninformative.
      The biological relevance to ATP5F1A function is unclear.
    supported_by:
    - reference_id: PMID:15324660
      supporting_text: >-
        Proteomic, functional, and domain-based analysis of in vivo 14-3-3
        binding proteins involved in cytoskeletal regulation and cellular
        organization.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19343720
  review:
    summary: >-
      IPI protein binding from a study identifying proteins interacting with SIRT1
      and SIRT3
      (Law et al. 2009). UniProt confirms SIRT3 interaction with ATP5F1A. SIRT3
      is
      a
      mitochondrial deacetylase that regulates the acetylation of OXPHOS components.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While the SIRT3 interaction is biologically meaningful (SIRT3 deacetylates
      ATP5F1A
      as part
      of mitochondrial metabolic regulation), the generic "protein binding" term
      is
      uninformative.
      A more specific term would be preferable.
    supported_by:
    - reference_id: PMID:19343720
      supporting_text: >-
        Identification and characterization of proteins interacting with SIRT1
        and SIRT3
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19688755
  review:
    summary: >-
      IPI protein binding from an LC-MS/MS study analyzing protein complexes by
      blue
      native
      analysis (Wessels et al. 2009). This likely detected ATP5F1A as part of intact
      Complex V.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Large-scale proteomic study. The detection of ATP5F1A in protein complexes
      is
      expected given
      that it is a subunit of Complex V. Generic protein binding is uninformative.
    supported_by:
    - reference_id: PMID:19688755
      supporting_text: >-
        LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of
        protein complexes.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20618440
  review:
    summary: >-
      IPI protein binding from proteomic analysis of 14-3-3-binding proteins during
      C2-ceramide-induced apoptosis (Pozuelo-Rubio 2010).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Another 14-3-3 interaction proteomics study. Generic protein binding is uninformative.
      The biological relevance to ATP5F1A function is unclear.
    supported_by:
    - reference_id: PMID:20618440
      supporting_text: >-
        Proteomic and biochemical analysis of 14-3-3-binding proteins during
        C2-ceramide-induced apoptosis.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22309213
  review:
    summary: >-
      IPI protein binding from a study identifying GCN5L1 (BLOC1S1) as a mitochondrial
      acetyltransferase component (Scott et al. 2012). UniProt confirms that ATP5F1A
      interacts
      with BLOC1S1 and that BLOC1S1 is required for acetylation of ATP5F1A. BLOC1S1
      promotes
      acetylation of SIRT3 respiratory chain targets.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interaction with BLOC1S1/GCN5L1 is biologically meaningful for mitochondrial
      acetylation
      regulation, but the generic "protein binding" term is uninformative. The study
      showed that
      GCN5L1 interacts with and promotes acetylation of respiratory chain targets,
      including
      ATP5F1A.
    supported_by:
    - reference_id: PMID:22309213
      supporting_text: >-
        GCN5L1 interacts with and promotes acetylation of SIRT3 respiratory chain
        targets and
        reverses global SIRT3 effects on mitochondrial protein acetylation, respiration
        and
        bioenergetics.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27499296
  review:
    summary: >-
      IPI protein binding from mitochondrial protein interaction mapping study (Floyd
      et al. 2016).
      Focused mitochondrial interactome study identifying regulators of respiratory
      chain function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While this is a mitochondria-focused interaction study, the generic protein
      binding term is
      uninformative. The study mapped mitochondrial protein interactions but the
      specific
      functional significance for ATP5F1A is not captured by this annotation.
    supported_by:
    - reference_id: PMID:27499296
      supporting_text: >-
        Mitochondrial Protein Interaction Mapping Identifies Regulators of
        Respiratory Chain Function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  review:
    summary: >-
      IPI protein binding from a large-scale human interactome mapping study (Huttlin
      et al. 2017).
      High-throughput study mapping the architecture of the human interactome.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Large-scale interactome study. Generic protein binding is uninformative for
      a well-characterized
      enzyme subunit.
    supported_by:
    - reference_id: PMID:28514442
      supporting_text: >-
        Architecture of the human interactome defines protein communities and
        disease networks.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30021884
  review:
    summary: >-
      IPI protein binding from a histone interaction landscape study using crosslinking
      mass
      spectrometry in intact cell nuclei (Fasci et al. 2018). ATP5F1A detected as
      a
      histone-interacting protein.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This study focused on histone interactions by crosslinking mass spectrometry.
      Detection
      of ATP5F1A likely reflects its abundance rather than a specific functional
      interaction
      with histones. Generic protein binding is uninformative.
    supported_by:
    - reference_id: PMID:30021884
      supporting_text: >-
        Histone Interaction Landscapes Visualized by Crosslinking Mass
        Spectrometry in Intact Cell Nuclei.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32814053
  review:
    summary: >-
      IPI protein binding from interactome mapping focused on neurodegenerative
      disease
      proteins
      (Haenig et al. 2020). UniProt documents an interaction with HTT (huntingtin).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Disease-focused interactome study. Generic protein binding is uninformative.
      The interaction
      with neurodegenerative disease proteins is likely not a core function of ATP5F1A.
    supported_by:
    - reference_id: PMID:32814053
      supporting_text: >-
        Interactome Mapping Provides a Network of Neurodegenerative Disease
        Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  review:
    summary: >-
      IPI protein binding from dual proteome-scale network study showing cell-specific
      remodeling
      of the human interactome (Huttlin et al. 2021).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Large-scale interactome study. Generic protein binding is uninformative.
    supported_by:
    - reference_id: PMID:33961781
      supporting_text: >-
        Through affinity-purification mass spectrometry, we have created two
        proteome-scale, cell-line-specific interaction networks.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  review:
    summary: >-
      IPI protein binding from multimodal cell maps study (2024). High-throughput
      study mapping
      structural and functional genomics.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Large-scale high-throughput study. Generic protein binding is uninformative
      for ATP5F1A.
    supported_by:
    - reference_id: PMID:40205054
      supporting_text: >-
        Multimodal cell maps as a foundation for structural and functional genomics.
# ============================================================
# IEA ANNOTATIONS FROM ENSEMBL COMPARA (GO_REF:0000107)
# ============================================================
- term:
    id: GO:0002020
    label: protease binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for MF based on Ensembl Compara ortholog transfer. Protease
      binding
      may
      relate to the interaction with angiostatin, a proteolytic fragment of plasminogen,
      which
      binds the alpha subunit on the cell surface (PMID:10077593).
    action: KEEP_AS_NON_CORE
    reason: >-
      This likely derives from the ecto-ATP synthase function where the alpha subunit
      binds
      angiostatin (a protease fragment of plasminogen) on the cell surface. While
      the interaction
      is experimentally documented (PMID:10077593), this is a secondary function
      associated
      with
      ecto-ATP synthase, not the core mitochondrial role.
    supported_by:
    - reference_id: PMID:10077593
      supporting_text: >-
        Angiostatin binds ATP synthase on the surface of human endothelial cells
- term:
    id: GO:0009986
    label: cell surface
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for CC based on Ensembl Compara. ATP5F1A is present on the
      cell
      surface as
      part of ecto-ATP synthase, demonstrated by flow cytometry and immunofluorescence
      (PMID:10077593).
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but represents a non-core localization. Cell surface presence relates
      to the
      ecto-ATP synthase function. Primary localization is mitochondrial. Experimentally
      supported
      by Moser et al. (PMID:10077593).
    supported_by:
    - reference_id: PMID:10077593
      supporting_text: >-
        The presence of this protein on the cell surface was confirmed by flow
        cytometry
        and immunofluorescence analysis.
- term:
    id: GO:0014850
    label: response to muscle activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for BP from Ensembl Compara ortholog transfer. This is a pleiotropic
      response
      annotation likely transferred from a model organism where ATP5F1A expression
      changes with
      muscle activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      While mitochondrial ATP synthase subunit expression could reasonably be modulated
      by muscle
      activity (given the high energy demand of muscle), this is a downstream response
      rather than
      a core function of ATP5F1A. It reflects the metabolic adaptation of the OXPHOS
      system to
      energy demands.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for CC from Ensembl Compara. Very broad term. ATP5F1A associates
      with
      multiple membranes (mitochondrial inner membrane, plasma membrane as ecto-ATP
      synthase).
    action: ACCEPT
    reason: >-
      Correct but very broad. ATP5F1A is a peripheral membrane protein associated
      with the
      mitochondrial inner membrane and cell surface membrane. More specific terms
      are annotated
      elsewhere.
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: contributes_to
  review:
    summary: >-
      IEA annotation for MF with contributes_to qualifier from Ensembl Compara.
      ATP
      hydrolysis
      is the reverse activity of ATP synthase, which can be activated in vitro.
      UniProt
      notes
      that in vivo the enzyme can only synthesize ATP, but its ATP hydrolase activity
      can be
      activated artificially in vitro.
    action: ACCEPT
    reason: >-
      The contributes_to qualifier is appropriate. The Complex V can hydrolyze ATP
      (the reverse
      reaction) and this is regulated by IF1 (ATPIF1). The alpha subunit contributes
      to this
      activity as part of the complex. UniProt states: "In vivo, can only synthesize
      ATP although
      its ATP hydrolase activity can be activated artificially in vitro." The immunocapture
      study
      (PMID:12110673) directly measured ATP hydrolysis activity of the purified
      complex.
    supported_by:
    - reference_id: PMID:12110673
      supporting_text: >-
        The captured complex V displayed ATP hydrolysis activity that was fully
        oligomycin
        and
        inhibitor protein IF(1)-sensitive.
- term:
    id: GO:0043531
    label: ADP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for MF from Ensembl Compara, duplicating the IBA annotation
      for
      the same
      GO term.
    action: ACCEPT
    reason: >-
      Correct and consistent with the IBA annotation. Duplicate evidence codes are
      fine. The alpha
      subunit binds ADP at its non-catalytic nucleotide-binding sites.
- term:
    id: GO:0045121
    label: membrane raft
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for CC from Ensembl Compara. Membrane raft localization may
      relate
      to the
      ecto-ATP synthase function on the cell surface.
    action: KEEP_AS_NON_CORE
    reason: >-
      This likely relates to the ecto-ATP synthase localization in lipid raft/membrane
      raft
      domains on the cell surface, which has been documented for ATP synthase subunits
      (PMID:17643490 shows co-localization with MHC-I in punctate membrane domains).
      This is
      a secondary localization associated with the ecto function.
    supported_by:
    - reference_id: PMID:17643490
      supporting_text: >-
        Confocal microscopy analysis of MHC-I and ecto-F1-ATPase beta chain expression
        on
        HepG2 cells shows a co-localization of both complexes in punctate membrane
        domains.
- term:
    id: GO:0045471
    label: response to ethanol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for BP from Ensembl Compara ortholog transfer. This is a broad
      response
      annotation likely reflecting that ATP synthase expression is modulated by
      ethanol
      exposure.
    action: KEEP_AS_NON_CORE
    reason: >-
      Ethanol affects mitochondrial function and OXPHOS complex expression, so ATP5F1A
      expression
      changes in response to ethanol are plausible but represent a downstream effect
      rather than
      a core function. This is a pleiotropic response annotation.
- term:
    id: GO:0071549
    label: cellular response to dexamethasone stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for BP from Ensembl Compara. Dexamethasone can modulate mitochondrial
      function and gene expression, including OXPHOS components.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic response annotation. Dexamethasone effects on ATP5F1A expression
      are a
      secondary consequence of glucocorticoid signaling on mitochondrial metabolism,
      not a core
      function.
- term:
    id: GO:0071732
    label: cellular response to nitric oxide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for BP from Ensembl Compara. Nitric oxide is known to inhibit
      mitochondrial
      respiration and can modify Complex V.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic response annotation. NO affects mitochondrial OXPHOS function,
      and
      Complex V
      subunit expression or modification may change in response. This is a downstream
      effect,
      not a core function of ATP5F1A.
# ============================================================
# IDA AND OTHER EXPERIMENTAL ANNOTATIONS
# ============================================================
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: >-
      IDA annotation for CC based on curation of immunofluorescence data. Mitochondrial
      localization confirmed by immunofluorescence.
    action: ACCEPT
    reason: >-
      Correct. Direct experimental evidence for mitochondrial localization via
      immunofluorescence. This is the primary localization for ATP5F1A.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: NAS
  original_reference_id: PMID:26297831
  review:
    summary: >-
      NAS annotation for CC citing the assembly study of human mitochondrial ATP
      synthase
      (Fujikawa et al. 2015). The study demonstrates that alpha subunits assemble
      into the
      F1-c-ring intermediate at the inner mitochondrial membrane.
    action: ACCEPT
    reason: >-
      Correct. The alpha subunit is part of the F1 head which is attached to the
      inner
      mitochondrial membrane via the central stalk connected to the Fo sector. The
      assembly
      study shows that F1 (containing alpha subunits) assembles with the c-ring
      as
      an
      intermediate (PMID:26297831).
    supported_by:
    - reference_id: PMID:26297831
      supporting_text: >-
        When expression of d-subunit, a stator stalk component, was knocked-down,
        human cells
        could not form ATP synthase holocomplex and instead accumulated two subcomplexes,
        one
        containing a central rotor shaft plus catalytic subunits (F1-c-ring)
- term:
    id: GO:0015986
    label: proton motive force-driven ATP synthesis
  evidence_type: NAS
  original_reference_id: PMID:26297831
  review:
    summary: >-
      NAS annotation for BP citing the assembly study. The study addresses assembly
      of the
      ATP synthase rather than directly demonstrating the proton motive force-driven
      ATP
      synthesis activity, but the function is well established.
    action: ACCEPT
    reason: >-
      While the cited study focuses on assembly, proton motive force-driven ATP
      synthesis
      is
      the core function of the complex that ATP5F1A assembles into. Well supported
      by other
      references.
    supported_by:
    - reference_id: PMID:26297831
      supporting_text: >-
        Mitochondrial ATP synthase is a motor enzyme in which a central shaft
        rotates
        in the
        stator casings fixed with the peripheral stator stalk.
- term:
    id: GO:0015986
    label: proton motive force-driven ATP synthesis
  evidence_type: IDA
  original_reference_id: PMID:37244256
  review:
    summary: >-
      IDA annotation for BP from the cryo-EM structure of human ATP synthase (Lai
      et al. 2023).
      The study resolved multiple rotational states demonstrating the proton motive
      force-driven
      ATP synthesis mechanism, with ATP5F1A visible as chains A/B/C.
    action: ACCEPT
    reason: >-
      Correct. The structural study directly visualizes the rotary mechanism of
      ATP
      synthesis in
      the human enzyme, with the alpha subunit forming part of the catalytic hexameric
      head.
      Represents core function.
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        Biological energy currency ATP is produced by F1Fo-ATP synthase. However,
        the molecular
        mechanism for human ATP synthase action remains unknown. Here, we present
        snapshot images
        for three main rotational states and one substate of human ATP synthase
- term:
    id: GO:0045259
    label: proton-transporting ATP synthase complex
  evidence_type: IDA
  original_reference_id: PMID:37244256
  review:
    summary: >-
      IDA annotation for CC from the cryo-EM structure of human ATP synthase. The
      study directly
      resolved ATP5F1A as part of the intact complex.
    action: ACCEPT
    reason: >-
      Direct structural evidence. The cryo-EM structure (PDB: 8H9E and others) shows
      ATP5F1A as
      chains A/B/C in the intact human ATP synthase complex.
    supported_by:
    - reference_id: PMID:37244256
      supporting_text: >-
        Structure of the human ATP synthase
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  review:
    summary: >-
      HTP annotation for CC from the quantitative high-confidence human mitochondrial
      proteome
      study (Morgenstern et al. 2021). ATP5F1A was identified with high confidence
      as part of
      the mitochondrial proteome.
    action: ACCEPT
    reason: >-
      Correct. This high-quality mitochondrial proteomics study provides strong
      quantitative
      evidence for mitochondrial localization. ATP5F1A is one of the most abundant
      mitochondrial
      proteins.
    supported_by:
    - reference_id: PMID:34800366
      supporting_text: >-
        We classified >8,000 proteins in mitochondrial preparations of human cells
        and
        defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP).
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IC
  original_reference_id: PMID:12110673
  review:
    summary: >-
      IC annotation for CC citing the immunocapture study (Aggeler et al. 2002).
      ATP5F1A
      was
      identified as a subunit of immunocaptured F1Fo from heart tissue and fibroblasts.
    action: ACCEPT
    reason: >-
      Correct. The immunocapture study isolated F1Fo from mitochondria, confirming
      the alpha
      subunit is a mitochondrial protein. The study identified ATP5F1A with specific
      antibodies.
    supported_by:
    - reference_id: PMID:12110673
      supporting_text: >-
        The immunoprecipitated F(1)F(0) contained a full complement of subunits
        that
        were
        identified with specific antibodies against five of the subunits (alpha,
        beta,
        OSCP,
        d, and IF(1))
- term:
    id: GO:0045259
    label: proton-transporting ATP synthase complex
  evidence_type: IDA
  original_reference_id: PMID:12110673
  review:
    summary: >-
      IDA annotation for CC from the immunocapture study. ATP5F1A was directly identified
      as
      a component of the purified ATP synthase complex from heart tissue and fibroblasts.
    action: ACCEPT
    reason: >-
      Direct experimental evidence. The alpha subunit was identified by specific
      antibodies
      in
      the immunocaptured F1Fo complex.
    supported_by:
    - reference_id: PMID:12110673
      supporting_text: >-
        The immunoprecipitated F(1)F(0) contained a full complement of subunits
        that
        were
        identified with specific antibodies against five of the subunits (alpha,
        beta,
        OSCP,
        d, and IF(1))
- term:
    id: GO:0046933
    label: proton-transporting ATP synthase activity, rotational mechanism
  evidence_type: IDA
  original_reference_id: PMID:12110673
  qualifier: contributes_to
  review:
    summary: >-
      IDA annotation for MF with contributes_to qualifier from the immunocapture
      study.
      The
      purified complex containing the alpha subunit displayed ATP hydrolysis activity
      (the reverse
      of ATP synthesis via the rotational mechanism), confirming the complex is
      functional.
    action: ACCEPT
    reason: >-
      Correct. The contributes_to qualifier is appropriate since the alpha subunit
      contributes
      to but does not itself catalyze the activity. The study directly measured
      ATP
      hydrolysis
      activity of the immunocaptured complex.
    supported_by:
    - reference_id: PMID:12110673
      supporting_text: >-
        The captured complex V displayed ATP hydrolysis activity that was fully
        oligomycin
        and
        inhibitor protein IF(1)-sensitive.
# ============================================================
# REACTOME TAS ANNOTATIONS - Mitochondrial matrix
# ============================================================
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-164832
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "ATPase synthesizes ATP". The
      F1
      head
      where ATP5F1A resides faces the mitochondrial matrix.
    action: ACCEPT
    reason: >-
      Correct. The F1 catalytic head, containing the alpha3-beta3 hexamer, faces
      the
      mitochondrial matrix. ATP5F1A is a matrix-exposed peripheral membrane protein.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-164834
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "Enzyme-bound ATP is released".
      Duplicate
      CC annotation from a different Reactome reaction. Correct.
    action: ACCEPT
    reason: >-
      Correct. Same localization from a different Reactome reaction in the ATP synthesis
      pathway. The alpha subunit is in the matrix-facing F1 head.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-164840
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "ADP and Pi bind to ATPase". Duplicate
      CC annotation from a different Reactome reaction. Correct.
    action: ACCEPT
    reason: >-
      Correct. Same localization from another Reactome reaction step. ADP and Pi
      binding
      occurs in the matrix-facing catalytic head.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8949580
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "F1Fo ATP synthase dimerizes".
      The
      dimerization occurs at the inner mitochondrial membrane, with the F1 head
      in
      the matrix.
    action: ACCEPT
    reason: >-
      Correct. ATP synthase dimerization is relevant to cristae formation and the
      alpha subunit
      is located in the matrix.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838035
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "CLPXP binds mitochondrial matrix
      proteins".
      ATP5F1A is a substrate of CLPXP protease in the mitochondrial matrix.
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A is a mitochondrial matrix-exposed protein that is recognized
      by CLPXP
      as a substrate for quality control/degradation.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838081
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "LONP1 degrades mitochondrial
      matrix
      proteins".
      ATP5F1A is a substrate of LONP1 protease in the matrix.
    action: ACCEPT
    reason: >-
      Correct. The matrix-facing F1 head exposes ATP5F1A to matrix proteases like
      LONP1 for
      quality control.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838093
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "LONP1 binds mitochondrial matrix
      proteins".
      Same context as above.
    action: ACCEPT
    reason: >-
      Correct. Duplicate CC annotation from the LONP1 binding step. ATP5F1A is in
      the
      mitochondrial matrix.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838289
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "CLPXP degrades mitochondrial
      matrix
      proteins".
    action: ACCEPT
    reason: >-
      Correct. Same localization from the CLPXP degradation reaction.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9839105
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "AFG3L2 degrades mitochondrial
      matrix
      proteins".
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A is exposed to matrix-side proteases for quality control.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9839149
  review:
    summary: >-
      TAS annotation for CC from Reactome pathway "AFG3L2 binds mitochondrial matrix
      proteins".
    action: ACCEPT
    reason: >-
      Correct. Same mitochondrial matrix localization from the AFG3L2 binding step.
# ============================================================
# EXPERIMENTAL ANNOTATIONS - Ecto-ATP synthase and functional studies
# ============================================================
- term:
    id: GO:0006754
    label: ATP biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IMP annotation for BP from the thymosin beta-4 study (Freeman et al. 2011).
      The study
      showed that thymosin beta-4 increases cell surface ATP levels via ATP synthase,
      demonstrating
      ATP biosynthetic process. Although evidence comes from ecto-ATP synthase,
      the
      GO term
      (ATP biosynthetic process) describes a core function of ATP5F1A.
    action: ACCEPT
    reason: >-
      The GO term GO:0006754 is correct for ATP5F1A. While the evidence comes from
      the ecto-ATP
      synthase context, ATP biosynthetic process is a core function of the gene.
      Consistent
      with
      IEA and NAS annotations to the same term.
    supported_by:
    - reference_id: PMID:21106936
      supporting_text: >-
        we have identified an extracellular signaling pathway where Tβ4 increases
        cell
        surface ATP levels via ATP synthase
- term:
    id: GO:0043536
    label: positive regulation of blood vessel endothelial cell migration
  evidence_type: IGI
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IGI annotation for BP from the thymosin beta-4 study. The study showed that
      thymosin beta-4
      promotes HUVEC migration through ecto-ATP synthase, with ATP-responsive P2X4
      receptor
      required for the migration effect. ATP5F1A participates as part of the ecto-ATP
      synthase
      complex.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a downstream effect of ecto-ATP synthase function. While the interaction
      is
      experimentally demonstrated, positive regulation of endothelial cell migration
      is mediated
      through extracellular ATP/purinergic signaling and is a non-core function
      of
      ATP5F1A.
    supported_by:
    - reference_id: PMID:21106936
      supporting_text: >-
        Silencing of the ATP-responsive purinergic receptor P2X4 with siRNA also
        blocked
        Tβ4-induced HUVEC migration in a transwell assay.
- term:
    id: GO:0042776
    label: proton motive force-driven mitochondrial ATP synthesis
  evidence_type: IDA
  original_reference_id: PMID:12110673
  review:
    summary: >-
      IDA annotation for BP from the immunocapture study (Aggeler et al. 2002).
      The
      purified
      complex containing ATP5F1A was functionally active with ATP hydrolysis (reverse
      of
      synthesis), demonstrating the complex's catalytic capability.
    action: ACCEPT
    reason: >-
      Correct. This is the most specific BP annotation for ATP5F1A's core function.
      The
      immunocapture study isolated functional F1Fo from human heart tissue and fibroblasts,
      containing the alpha subunit, and demonstrated catalytic activity. While the
      alpha
      subunit is the non-catalytic subunit, it is essential for the process.
    supported_by:
    - reference_id: PMID:12110673
      supporting_text: >-
        The captured complex V displayed ATP hydrolysis activity that was fully
        oligomycin
        and inhibitor protein IF(1)-sensitive.
- term:
    id: GO:0045259
    label: proton-transporting ATP synthase complex
  evidence_type: IDA
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IDA annotation for CC from the thymosin beta-4 study. The study identified
      F1-F0
      ATP
      synthase as a target of thymosin beta-4 by pulldown and mass spectrometry,
      with
      ATP5F1A as part of the complex.
    action: ACCEPT
    reason: >-
      Correct. The study directly identified F1-F0 ATP synthase components by mass
      spectrometry,
      confirming ATP5F1A as a complex member.
    supported_by:
    - reference_id: PMID:21106936
      supporting_text: >-
        we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin
- term:
    id: GO:0046933
    label: proton-transporting ATP synthase activity, rotational mechanism
  evidence_type: IMP
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IMP annotation for MF from the thymosin beta-4 study (Freeman et al. 2011).
      The study
      showed that oligomycin (an ATP synthase inhibitor) blocked the thymosin beta-4-induced
      increase in cell surface ATP levels, demonstrating ATP synthase activity.
      Although
      the
      evidence comes from ecto-ATP synthase on the cell surface, the GO term itself
      (proton-
      transporting ATP synthase activity, rotational mechanism) is a core function
      of ATP5F1A.
    action: ACCEPT
    reason: >-
      The GO term GO:0046933 is correct for ATP5F1A regardless of whether evidence
      comes from
      mitochondrial or ecto-ATP synthase context. The term describes the molecular
      activity of
      the complex, which is a core function. The alpha subunit contributes to this
      activity via
      non-catalytic nucleotide binding sites. Consistent with IBA, IEA, IDA, and
      ISS
      annotations
      to the same term.
    supported_by:
    - reference_id: PMID:21106936
      supporting_text: >-
        Blocking antibodies and antagonists (oligomycin, IC(50) ∼1.8 μM;
        piceatannol, IC(50) ∼1.05 μM; and angiostatin, IC(50) ∼2.9 μg/ml) of ATP
        synthase inhibited the Tβ4-induced increase in cell surface ATP levels,
        as
        measured by luciferase assay, and the Tβ4-induced increase in HUVEC migration,
        as measured by transwell migration assay
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IPI protein binding from the thymosin beta-4 study. The study identified the
      interaction
      between thymosin beta-4 and F1-F0 ATP synthase by pulldown experiments. However,
      the
      binding was specifically to the beta subunit (K_D 12 nM), not the alpha subunit.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The study primarily demonstrates thymosin beta-4 binding to the beta subunit
      of ATP synthase
      (K_D 12 nM by SPR). The alpha subunit was co-isolated as part of the complex
      but was not
      shown to be the direct binding partner. Generic protein binding is uninformative.
    supported_by:
    - reference_id: PMID:21106936
      supporting_text: >-
        By surface plasmon resonance, we determined for Tβ4 binding to the β subunit
        of
        ATP synthase a K(D) of 12 nM.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IDA
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IDA annotation for CC from the thymosin beta-4 study. This likely refers to
      the cell surface
      membrane where ecto-ATP synthase is found.
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A is associated with membranes -- both the mitochondrial inner
      membrane and
      the plasma membrane (as ecto-ATP synthase). Very broad but acceptable.
    supported_by:
    - reference_id: PMID:21106936
      supporting_text: >-
        we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin
- term:
    id: GO:0043532
    label: angiostatin binding
  evidence_type: IPI
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IPI annotation for MF from the thymosin beta-4 study. However, this annotation
      appears
      incorrectly attributed to this reference. The original angiostatin binding
      to
      ATP5F1A was
      demonstrated in PMID:10077593 (Moser et al. 1999), where angiostatin was shown
      to bind the
      alpha/beta subunits of ATP synthase on the cell surface.
    action: KEEP_AS_NON_CORE
    reason: >-
      Angiostatin binding to ATP5F1A is well documented (PMID:10077593) and confirmed
      by multiple
      studies. However, it is a non-core function related to ecto-ATP synthase.
      The
      referenced
      study (PMID:21106936) does mention angiostatin as an ATP synthase antagonist
      but the
      primary evidence for angiostatin binding to the alpha subunit comes from PMID:10077593.
    supported_by:
    - reference_id: PMID:10077593
      supporting_text: >-
        Angiostatin also bound to the recombinant alpha-subunit of human ATP synthase,
        and
        this binding was not inhibited by a 2,500-fold molar excess of plasminogen.
    - reference_id: PMID:21106936
      supporting_text: >-
        we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11741979
  review:
    summary: >-
      IPI protein binding from the p43/EMAP II study (Chang et al. 2002). The study
      demonstrated
      that EMAP II (C-terminal domain of p43) binds the alpha subunit of ATP synthase
      on the cell
      surface and inhibits endothelial cell proliferation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interaction with EMAP II is specific and functionally characterized (EMAP
      II binds
      cell-surface alpha-ATP synthase and inhibits endothelial cell growth). However,
      the generic
      "protein binding" term is uninformative. This is also a non-core ecto-ATP
      synthase
      function.
    supported_by:
    - reference_id: PMID:11741979
      supporting_text: >-
        The isolated protein was determined to be the alpha subunit of ATP synthase.
        The
        interaction of EMAP II and alpha-ATP synthase was confirmed by enzyme-linked
        immunosorbent assay and in vitro pull down assays
# ============================================================
# HDA ANNOTATIONS (High-throughput Direct Assay)
# ============================================================
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:23533145
  review:
    summary: >-
      HDA annotation for CC from in-depth proteomic analysis of exosomes isolated
      from expressed
      prostatic secretions in urine. ATP5F1A was identified in exosomal fractions.
    action: KEEP_AS_NON_CORE
    reason: >-
      Detection of ATP5F1A in extracellular exosomes is consistent with its abundance
      and the
      known presence of mitochondrial proteins in exosomes. This is a non-core localization.
    supported_by:
    - reference_id: PMID:23533145
      supporting_text: >-
        In-depth proteomic analyses of exosomes isolated from expressed prostatic
        secretions in urine.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:19946888
  review:
    summary: >-
      HDA annotation for CC from a study defining the membrane proteome of NK cells.
      ATP5F1A
      was identified in the membrane fraction.
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A is a membrane-associated protein (mitochondrial inner membrane
      and
      potentially cell surface). Detection in the membrane proteome is expected.
    supported_by:
    - reference_id: PMID:19946888
      supporting_text: >-
        Defining the membrane proteome of NK cells.
- term:
    id: GO:0003723
    label: RNA binding
  evidence_type: HDA
  original_reference_id: PMID:22658674
  review:
    summary: >-
      HDA annotation for MF from the mammalian mRNA-binding protein atlas study
      (Castello
      et al.
      2012). ATP5F1A was detected as an mRNA-binding protein in this large-scale
      UV
      crosslinking
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This is from a large-scale UV crosslinking study that identified thousands
      of
      mRNA-binding
      proteins. Many abundant proteins are detected in such screens due to non-specific
      crosslinking.
      RNA binding is not a characterized function of ATP5F1A and is likely an artifact
      of the
      protein's high abundance.
    supported_by:
    - reference_id: PMID:22658674
      supporting_text: >-
        Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HDA
  original_reference_id: PMID:20833797
  review:
    summary: >-
      HDA annotation for CC from a phosphoproteome analysis of functional mitochondria
      isolated
      from resting human muscle (Zhao et al. 2011). ATP5F1A was identified as a
      phosphorylated
      mitochondrial protein.
    action: ACCEPT
    reason: >-
      Correct. ATP5F1A was identified in functional mitochondria from human muscle,
      consistent
      with its well-established mitochondrial localization and known phosphorylation
      sites
      (UniProt documents multiple phosphoserine sites).
    supported_by:
    - reference_id: PMID:20833797
      supporting_text: >-
        We performed a phosphoproteomics study of functional mitochondria isolated
        from human muscle biopsies
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:19056867
  review:
    summary: >-
      HDA annotation for CC from large-scale proteomics and phosphoproteomics of
      urinary
      exosomes. ATP5F1A was identified in exosomal fractions.
    action: KEEP_AS_NON_CORE
    reason: >-
      Detection in urinary exosomes is consistent with the abundance of ATP5F1A
      and
      the known
      presence of mitochondrial proteins in exosomal fractions. Non-core localization.
    supported_by:
    - reference_id: PMID:19056867
      supporting_text: >-
        Large-scale proteomics and phosphoproteomics of urinary exosomes.
# ============================================================
# ADDITIONAL EXPERIMENTAL ANNOTATIONS
# ============================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19285951
  review:
    summary: >-
      IPI protein binding from a study demonstrating that histidine-rich glycoprotein
      (HRG)
      interacts with the alpha subunit of ATP synthase on the surface of T-cells
      (Ohta
      et al.
      2009). The interaction was specific (K_D 66 nM) and mediates HRG/Con A-induced
      morphological changes.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The HRG-ATP5F1A interaction is specific and well-characterized (K_D 66 nM).
      However,
      generic "protein binding" is uninformative. This is an ecto-ATP synthase interaction.
      UniProt confirms: "Interacts with HRG; the interaction occurs on the surface
      of T-cells."
    supported_by:
    - reference_id: PMID:19285951
      supporting_text: >-
        HRG specifically interacted with mitochondrial ATP synthase with a dissociation
        constant of 66 nM.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IDA
  original_reference_id: PMID:19016746
  review:
    summary: >-
      IDA annotation for CC from a study identifying galectin-3 interaction with
      mitochondrial
      F1F0-ATP synthase in colon cancer cells (Kim et al. 2008). The study showed
      that
      galectin-3 and ATP synthase co-localized in the inner membrane vesicles of
      mitochondria.
    action: ACCEPT
    reason: >-
      Correct. The study demonstrated by subcellular fractionation that ATP synthase
      is in the
      inner mitochondrial membrane, co-localized with galectin-3.
    supported_by:
    - reference_id: PMID:19016746
      supporting_text: >-
        Galectin-3 and ATP synthase were co-isolated in the inner membrane vesicles
        of
        mitochondria.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for MF based on manual transfer from ortholog by curator judgment.
      ATP
      binding is well established for the alpha subunit at its non-catalytic nucleotide-binding
      sites.
    action: ACCEPT
    reason: >-
      Correct. The alpha subunit binds ATP at non-catalytic regulatory sites. Well
      supported
      by structural evidence (PMID:37244256) and UniProt binding site annotations.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: NAS
  original_reference_id: PMID:1830491
  review:
    summary: >-
      NAS annotation for CC citing the original cDNA cloning paper for the alpha
      subunit
      (Kataoka & Biswas 1991). The paper describes cloning the cDNA for the alpha
      subunit of
      human mitochondrial ATP synthase.
    action: ACCEPT
    reason: >-
      Correct. The original cloning paper established the identity of this gene
      as
      encoding
      the alpha subunit of mitochondrial ATP synthase.
    supported_by:
    - reference_id: PMID:1830491
      supporting_text: >-
        A full length cDNA clone of the alpha subunit of mitochondrial ATP synthase
        (EC
        3.6.1.34) has been isolated from a cDNA library prepared from LX-1 human
        tumor
        cells
- term:
    id: GO:0006629
    label: lipid metabolic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for BP based on ortholog transfer. Lipid metabolic process
      may
      relate to
      the ecto-ATP synthase role in HDL/apolipoprotein metabolism, where cell surface
      ATP synthase
      is involved in HDL endocytosis.
    action: KEEP_AS_NON_CORE
    reason: >-
      This likely refers to the ecto-ATP synthase function in HDL metabolism. Cell-surface
      ATP
      synthase has been implicated in apolipoprotein A-I-stimulated HDL endocytosis
      in hepatocytes.
      While this is a legitimate function, it is secondary to the core mitochondrial
      role.
- term:
    id: GO:0006754
    label: ATP biosynthetic process
  evidence_type: NAS
  original_reference_id: PMID:1830491
  review:
    summary: >-
      NAS annotation for BP citing the original cDNA cloning paper. The paper describes
      ATP5F1A
      as a subunit of mitochondrial ATP synthase, implying its role in ATP biosynthesis.
    action: ACCEPT
    reason: >-
      Correct. The original paper identified this gene as encoding a subunit of
      ATP
      synthase
      (EC 3.6.1.34), which is responsible for ATP biosynthesis.
    supported_by:
    - reference_id: PMID:1830491
      supporting_text: >-
        A full length cDNA clone of the alpha subunit of mitochondrial ATP synthase
        (EC
        3.6.1.34) has been isolated
- term:
    id: GO:0046933
    label: proton-transporting ATP synthase activity, rotational mechanism
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for MF based on ortholog transfer. The proton-transporting
      ATP
      synthase
      activity is well established for this complex. Note this annotation lacks
      the
      contributes_to
      qualifier that is appropriate for the alpha subunit.
    action: ACCEPT
    reason: >-
      Correct term. Ideally should have the contributes_to qualifier for the alpha
      subunit since
      catalytic activity resides in the beta subunit, but as an ISS the annotation
      is acceptable.
- term:
    id: GO:0042288
    label: MHC class I protein binding
  evidence_type: IDA
  original_reference_id: PMID:17643490
  review:
    summary: >-
      IDA annotation for MF from the study showing close association between ecto-F1-ATPase
      and MHC class I on cell membranes (Vantourout et al. 2008). The study demonstrated
      that
      biotinylated F1-ATPase cell surface components co-immunoprecipitate with MHC-I
      molecules
      and co-localize in punctate membrane domains.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a specific and experimentally supported annotation related to the
      ecto-ATP
      synthase
      function. MHC class I association is relevant to immune recognition (gamma/delta
      T cell
      activation) and represents a specialized function on the cell surface. Non-core
      relative
      to the primary mitochondrial function.
    supported_by:
    - reference_id: PMID:17643490
      supporting_text: >-
        biotinylated F1-ATPase cell surface components co-immunoprecipitate with
        MHC-I
        molecules
        confirming the association of both complexes on Raji cells. Confocal microscopy
        analysis
        of MHC-I and ecto-F1-ATPase beta chain expression on HepG2 cells shows
        a co-localization
        of both complexes in punctate membrane domains.
# ============================================================
# ECTO-ATP SYNTHASE EXPERIMENTAL ANNOTATIONS
# ============================================================
- term:
    id: GO:0001937
    label: negative regulation of endothelial cell proliferation
  evidence_type: IMP
  original_reference_id: PMID:10077593
  review:
    summary: >-
      IMP annotation for BP from the angiostatin binding study (Moser et al. 1999).
      The study
      showed that angiostatin binding to ATP synthase alpha/beta subunits on the
      cell
      surface
      mediates its antiproliferative effect, which was inhibited by anti-alpha-subunit
      antibody.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a well-documented ecto-ATP synthase function. Angiostatin binding
      to
      cell surface
      ATP5F1A mediates inhibition of endothelial cell proliferation. However, this
      is a
      non-core function related to the ecto-ATP synthase role, not the primary mitochondrial
      function.
    supported_by:
    - reference_id: PMID:10077593
      supporting_text: >-
        Angiostatin's antiproliferative effect on endothelial cells was inhibited
        by as much
        as 90% in the presence of anti-alpha-subunit ATP synthase antibody.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IDA
  original_reference_id: PMID:10077593
  review:
    summary: >-
      IDA annotation for CC from the angiostatin study. Direct experimental evidence
      for
      plasma membrane localization by flow cytometry and immunofluorescence.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct. The study provided direct evidence for cell surface/plasma membrane
      localization
      using flow cytometry and immunofluorescence. This is the ecto-ATP synthase
      localization,
      secondary to mitochondrial localization.
    supported_by:
    - reference_id: PMID:10077593
      supporting_text: >-
        The presence of this protein on the cell surface was confirmed by flow
        cytometry
        and
        immunofluorescence analysis.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10077593
  review:
    summary: >-
      IPI protein binding from the angiostatin study. The study demonstrated specific
      binding
      of angiostatin to the alpha/beta subunits of ATP synthase on the cell surface,
      and
      confirmed binding to recombinant alpha subunit.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The interaction with angiostatin is specific and well-characterized. However,
      generic
      "protein binding" is uninformative. The more specific GO:0043532 (angiostatin
      binding) is
      already annotated for this gene, making this generic annotation redundant.
    supported_by:
    - reference_id: PMID:10077593
      supporting_text: >-
        Angiostatin also bound to the recombinant alpha-subunit of human ATP synthase,
        and
        this binding was not inhibited by a 2,500-fold molar excess of plasminogen.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with 
    GO terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to
    orthologs by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular 
    Location vocabulary mapping, accompanied by conservative changes to GO terms
    applied by UniProt
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data
    to orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning 
    models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10077593
  title: Angiostatin binds ATP synthase on the surface of human endothelial 
    cells.
  findings:
  - statement: >-
      ATP5F1A identified as the angiostatin binding protein on endothelial cell
      surface
      by
      N-terminal sequencing, peptide mass fingerprinting, and immunologic analyses.
      Angiostatin
      bound recombinant alpha subunit with binding not inhibited by plasminogen.
      Anti-alpha-subunit
      antibody blocked angiostatin's antiproliferative effect by 90%.
    supporting_text: >-
      The presence of this protein on the cell surface was confirmed by flow cytometry
      and
      immunofluorescence analysis.
- id: PMID:11410595
  title: Atp11p and Atp12p are assembly factors for the F(1)-ATPase in human 
    mitochondria.
  findings:
  - statement: >-
      ATPAF2 (Atp12p) is an assembly factor for the F1 component, interacting
      with
      the alpha
      subunit to facilitate F1 assembly.
    supporting_text: >-
      Atp11p and Atp12p were first described as proteins required for assembly
      of
      the F(1)
      component of the mitochondrial ATP synthase in Saccharomyces cerevisiae
- id: PMID:11741979
  title: Interaction of the C-terminal domain of p43 and the alpha subunit of 
    ATP synthase. Its functional implication in endothelial cell proliferation.
  findings:
  - statement: >-
      EMAP II binds the alpha subunit of ATP synthase on the cell surface. The
      interaction
      inhibits endothelial cell proliferation. Soluble alpha-ATP synthase relieves
      the
      antiproliferative effect.
    supporting_text: >-
      The isolated protein was determined to be the alpha subunit of ATP synthase.
      The
      interaction of EMAP II and alpha-ATP synthase was confirmed by enzyme-linked
      immunosorbent assay and in vitro pull down assays
- id: PMID:12110673
  title: A functionally active human F1F0 ATPase can be purified by 
    immunocapture from heart tissue and fibroblast cell lines. Subunit structure
    and activity studies.
  findings:
  - statement: >-
      F1F0 ATP synthase immunocaptured from human heart tissue and fibroblasts
      contained
      a full
      complement of subunits including alpha, beta, OSCP, d, and IF1. The captured
      complex
      displayed oligomycin-sensitive and IF1-sensitive ATP hydrolysis activity.
    supporting_text: >-
      The immunoprecipitated F(1)F(0) contained a full complement of subunits
      that
      were
      identified with specific antibodies against five of the subunits (alpha,
      beta,
      OSCP,
      d, and IF(1))
- id: PMID:15161933
  title: Comprehensive proteomic analysis of interphase and mitotic 
    14-3-3-binding proteins.
  findings: []
- id: PMID:15324660
  title: Proteomic, functional, and domain-based analysis of in vivo 14-3-3 
    binding proteins involved in cytoskeletal regulation and cellular 
    organization.
  findings: []
- id: PMID:17643490
  title: Ecto-F1-ATPase and MHC-class I close association on cell membranes.
  findings:
  - statement: >-
      Ecto-F1-ATPase (including alpha and beta chains) co-immunoprecipitates and
      co-localizes
      with MHC class I molecules in punctate membrane domains. Ecto-F1-ATPase
      epitope
      detection
      inversely correlates with MHC-I expression level.
    supporting_text: >-
      biotinylated F1-ATPase cell surface components co-immunoprecipitate with
      MHC-I
      molecules
      confirming the association of both complexes on Raji cells.
- id: PMID:1830491
  title: Nucleotide sequence of a cDNA for the alpha subunit of human 
    mitochondrial ATP synthase.
  findings:
  - statement: >-
      Original cDNA cloning of the human ATP5F1A gene. Encoded polypeptide of
      553
      residues
      highly homologous to ATP synthase alpha subunit from other species.
    supporting_text: >-
      A full length cDNA clone of the alpha subunit of mitochondrial ATP synthase
      (EC
      3.6.1.34) has been isolated
- id: PMID:19016746
  title: Identification of mitochondrial F(1)F(0)-ATP synthase interacting with 
    galectin-3 in colon cancer cells.
  findings:
  - statement: >-
      Galectin-3 co-localizes with ATP synthase in the inner membrane vesicles
      of
      mitochondria
      and has an inhibitory activity against ATP synthase.
    supporting_text: >-
      Galectin-3 and ATP synthase were co-isolated in the inner membrane vesicles
      of
      mitochondria.
- id: PMID:19056867
  title: Large-scale proteomics and phosphoproteomics of urinary exosomes.
  findings: []
- id: PMID:19285951
  title: High affinity interaction between histidine-rich glycoprotein and the 
    cell surface type ATP synthase on T-cells.
  findings:
  - statement: >-
      HRG binds the alpha subunit of ATP synthase on the surface of T-cells with
      K_D
      of 66 nM.
      The HRG/Con A-induced morphological changes of MOLT-4 cells were specifically
      inhibited by
      anti-beta-subunit antibody.
    supporting_text: >-
      HRG specifically interacted with mitochondrial ATP synthase with a dissociation
      constant of 66 nM.
- id: PMID:19343720
  title: 'Identification and characterization of proteins interacting with SIRT1 and
    SIRT3: implications in the anti-aging and metabolic effects of sirtuins.'
  findings: []
- id: PMID:19688755
  title: LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of 
    protein complexes.
  findings: []
- id: PMID:19946888
  title: Defining the membrane proteome of NK cells.
  findings: []
- id: PMID:20618440
  title: Proteomic and biochemical analysis of 14-3-3-binding proteins during 
    C2-ceramide-induced apoptosis.
  findings: []
- id: PMID:20833797
  title: Phosphoproteome analysis of functional mitochondria isolated from 
    resting human muscle reveals extensive phosphorylation of inner membrane 
    protein complexes and enzymes.
  findings: []
- id: PMID:21106936
  title: Regenerative protein thymosin beta-4 is a novel regulator of purinergic
    signaling.
  findings:
  - statement: >-
      Thymosin beta-4 binds the beta subunit of ecto-ATP synthase (K_D 12 nM)
      and
      increases
      cell surface ATP levels. Blocking antibodies and antagonists (oligomycin,
      piceatannol,
      angiostatin) inhibited the effect. P2X4 receptor mediates downstream migration.
    supporting_text: >-
      we identified F1-F0 ATP synthase, a known target of antiangiogenic angiostatin
- id: PMID:22309213
  title: 'Identification of a molecular component of the mitochondrial acetyltransferase
    programme: a novel role for GCN5L1.'
  findings:
  - statement: >-
      GCN5L1 (BLOC1S1) is a mitochondrial acetyltransferase that interacts with
      and
      promotes
      acetylation of SIRT3 respiratory chain targets including ATP5F1A. GCN5L1
      reverses
      global
      SIRT3 effects on mitochondrial protein acetylation.
    supporting_text: >-
      GCN5L1 interacts with and promotes acetylation of SIRT3 respiratory chain
      targets
      and
      reverses global SIRT3 effects on mitochondrial protein acetylation, respiration
      and
      bioenergetics.
- id: PMID:22658674
  title: Insights into RNA biology from an atlas of mammalian mRNA-binding 
    proteins.
  findings: []
- id: PMID:23533145
  title: In-depth proteomic analyses of exosomes isolated from expressed 
    prostatic secretions in urine.
  findings: []
- id: PMID:26297831
  title: Assembly of human mitochondrial ATP synthase through two separate 
    intermediates, F1-c-ring and b-e-g complex.
  findings:
  - statement: >-
      ATP synthase assembles through two intermediates: F1-c-ring (containing
      alpha,
      beta, and
      other catalytic subunits with the central rotor) and the b-e-g stator complex.
      The central
      rotor shaft and stator stalk form separately and assemble later.
    supporting_text: >-
      Assembly of human mitochondrial ATP synthase through two separate intermediates,
      F1-c-ring and b-e-g complex.
- id: PMID:27499296
  title: Mitochondrial Protein Interaction Mapping Identifies Regulators of 
    Respiratory Chain Function.
  findings: []
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and 
    disease networks.
  findings: []
- id: PMID:30021884
  title: Histone Interaction Landscapes Visualized by Crosslinking Mass 
    Spectrometry in Intact Cell Nuclei.
  findings: []
- id: PMID:32814053
  title: Interactome Mapping Provides a Network of Neurodegenerative Disease 
    Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
  findings: []
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the 
    human interactome.
  findings: []
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its 
    dynamics in cellular context.
  findings: []
- id: PMID:37244256
  title: Structure of the human ATP synthase.
  findings:
  - statement: >-
      Cryo-EM structures of human ATP synthase in three main rotational states
      and
      one substate.
      Alpha subunit (chains A/B/C) alternates with beta subunit (chains D/E/F)
      in
      the F1 head.
      Structures reveal ADP release mechanism, symmetry mismatch accommodation,
      and
      water
      molecules in proton channels. Clinically relevant mutations mapped to subunit
      interfaces.
    supporting_text: >-
      Structure of the human ATP synthase.
- id: file:human/ATP5F1A/ATP5F1A-deep-research-falcon.md
  title: Falcon deep research synthesis for ATP5F1A
  findings:
  - statement: Deep research synthesis confirms ATP5F1A as the alpha subunit of 
      human Complex V.
    supporting_text: >-
      ATP5F1A encodes the alpha subunit of the mitochondrial F1 sector of
      F1FO-ATP synthase (Complex V) in Homo sapiens
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional 
    genomics.
  findings: []
- id: Reactome:R-HSA-164832
  title: ATPase synthesizes ATP
  findings: []
- id: Reactome:R-HSA-164834
  title: Enzyme-bound ATP is released
  findings: []
- id: Reactome:R-HSA-164840
  title: ADP and Pi bind to ATPase
  findings: []
- id: Reactome:R-HSA-8949580
  title: F1Fo ATP synthase dimerizes
  findings: []
- id: Reactome:R-HSA-9838035
  title: CLPXP binds mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9838081
  title: LONP1 degrades mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9838093
  title: LONP1 binds mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9838289
  title: CLPXP degrades mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9839105
  title: AFG3L2 degrades mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9839149
  title: AFG3L2 binds mitochondrial matrix proteins
  findings: []
core_functions:
- molecular_function:
    id: GO:0005524
    label: ATP binding
  contributes_to_molecular_function:
    id: GO:0046933
    label: proton-transporting ATP synthase activity, rotational mechanism
  directly_involved_in:
  - id: GO:0042776
    label: proton motive force-driven mitochondrial ATP synthesis
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  in_complex:
    id: GO:0045259
    label: proton-transporting ATP synthase complex
  description: >-
    ATP5F1A is the non-catalytic alpha subunit of the F1 head of mitochondrial ATP
    synthase
    (Complex V). Three alpha subunits alternate with three beta subunits to form
    the
    alpha3-beta3 hexameric F1 catalytic head on the matrix side of the inner mitochondrial
    membrane. The alpha subunit binds ATP and ADP at non-catalytic regulatory sites
    that
    are essential for the rotational binding-change mechanism, but does NOT itself
    catalyze
    ATP synthesis -- the catalytic sites reside on the beta subunit (ATP5F1B). ATP5F1A
    therefore contributes_to the complex-level proton-transporting ATP synthase
    activity
    (GO:0046933) but does not independently enable it. The alpha subunit also plays
    a
    structural role in maintaining the integrity of the F1 head and accommodating
    the
    symmetry mismatch between the three-fold F1 and the c-ring rotor. Pathogenic
    variants
    (R207H, R329C, Y321C) cause severe Complex V deficiency (MC5DN4A/B). Cryo-EM
    structures
    at 2.4-2.9 A resolution (PMID:37244256) reveal three alpha chains (A/B/C) alternating
    with three beta chains (D/E/F), with clinically relevant mutations mapping to
    subunit
    interfaces. ATP synthase assembles through two intermediates: the F1-c-ring
    and
    the
    b-e-g stator complex (PMID:26297831). ATP5F1A also participates in ecto-ATP
    synthase
    activity on the cell surface, where it interacts with angiostatin (PMID:10077593),
    HRG (PMID:19285951), and EMAP II (PMID:11741979), but this is a non-core function.
  supported_by:
  - reference_id: PMID:37244256
    supporting_text: >-
      Alpha subunit (chains A/B/C) alternates with beta subunit (chains D/E/F)
      in
      the F1
      head. Structures reveal ADP release mechanism, symmetry mismatch accommodation,
      and
      water molecules in proton channels. Clinically relevant mutations mapped
      to
      subunit
      interfaces.
    full_text_unavailable: true
  - reference_id: PMID:26297831
    supporting_text: >-
      ATP synthase assembles through two intermediates: F1-c-ring (containing
      alpha,
      beta,
      and other catalytic subunits with the central rotor) and the b-e-g stator
      complex.
    full_text_unavailable: true
  - reference_id: PMID:12110673
    supporting_text: >-
      The captured complex V displayed ATP hydrolysis activity that was fully oligomycin
      and inhibitor protein IF(1)-sensitive

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

Falcon

Citations

📄 View Raw YAML