ATP6V1F encodes the F subunit (~13 kDa; 119 aa, 13,441 Da, historically called the "14-kDa subunit") of the V1 peripheral sector of the vacuolar-type H+-ATPase (V-ATPase). Together with subunit D, subunit F forms the central rotor of V1 that is driven by ATP hydrolysis in the catalytic A3B3 hexamer and transmits rotational energy to the V0 proteolipid c-ring to drive proton translocation across organelle membranes. ATP6V1F is the smallest subunit of V1 and is ubiquitously expressed, reflecting the housekeeping role of V-ATPase in acidifying lysosomes, endosomes, Golgi apparatus, and other organelles. The D-F central rotor assembly serves as the mechanical connection between the ATP-hydrolyzing head and the proton-translocating V0 membrane sector. In some cell types, the V-ATPase is targeted to the plasma membrane for extracellular acidification. The protein interacts directly with V0 d subunit (ATP6V0D1), cementing its position in the central stalk. Two alternatively spliced isoforms exist.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016020 membrane | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phylogenetic inference placing ATP6V1F as active in membrane context. The V1 F subunit is a peripheral protein on the cytoplasmic face of membranes where V-ATPase is active. Reason: The generic membrane annotation with is_active_in is subsumed by the more specific lysosomal membrane and other organelle membrane annotations. The IBA annotation is overly broad. |
| GO:0030665 clathrin-coated vesicle membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular location vocabulary mapping from ortholog data. V-ATPase is present on clathrin-coated vesicles for endocytic pathway acidification. Reason: Consistent with V-ATPase biology but non-core relative to lysosomal function. |
| GO:0030672 synaptic vesicle membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular location vocabulary mapping for synaptic vesicle membrane. V-ATPase acidifies synaptic vesicles for neurotransmitter loading. Reason: Non-core for this ubiquitously expressed subunit; neuronal context is secondary to the primary lysosomal function. |
| GO:0033180 proton-transporting V-type ATPase, V1 domain | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation placing ATP6V1F in the V1 domain. Confirmed by human cryo-EM structural data. Reason: Subunit F is a defining structural component of the V1 domain central rotor, confirmed by cryo-EM (PMID:33065002) and biochemical data (PMID:18752060). Supporting Evidence: PMID:33065002 Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. |
| GO:0034220 monoatomic ion transmembrane transport | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro-based annotation for monoatomic ion transmembrane transport, which subsumes proton transport. The more specific proton transmembrane transport annotation is more informative. Reason: The generic monoatomic ion transmembrane transport is subsumed by the more specific proton transmembrane transport annotations. Redundant and less informative. |
| GO:0046961 proton-transporting ATPase activity, rotational mechanism | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation for rotational ATPase activity. The F subunit is part of the central rotor essential for this activity. Reason: Core molecular function of the V-ATPase; subunit F is an essential structural component of the rotary mechanism. Supporting Evidence: PMID:18752060 Energy from this reaction drives the rotation of a central stalk consisting of V1 subunits D and F and this is coupled to rotation of the V0 proteolipid ring made up of c, c′ and c″. |
| GO:1902600 proton transmembrane transport | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation for proton transmembrane transport. Reason: Core biological process of V-ATPase. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Generic protein binding from a reference map of the human binary protein interactome. High-throughput; not informative for specific function. Reason: High-throughput interactome protein binding annotation is uninformative for the specific function of ATP6V1F. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Generic protein binding from a dual proteome-scale interactome network. High-throughput; not informative. Reason: High-throughput interactome data is uninformative for ATP6V1F function. |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | MARK AS OVER ANNOTATED | Summary: Generic protein binding from the OpenCell endogenous tagging study. High-throughput; not informative. Reason: High-throughput protein binding annotation is uninformative. |
| GO:0015078 proton transmembrane transporter activity | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl ortholog-transfer annotation for proton transmembrane transporter activity. The contributes_to qualifier appropriately acknowledges the whole-complex nature of this activity. Reason: Core molecular function of V-ATPase; contributes_to qualifier is appropriate for a structural subunit that participates in but does not individually perform the activity. |
| GO:0033176 proton-transporting V-type ATPase complex | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl ortholog-transfer annotation for V-type ATPase complex membership. Consistent with structural evidence. Reason: Core complex membership. |
| GO:0097401 synaptic vesicle lumen acidification | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ensembl ortholog-transfer annotation for synaptic vesicle lumen acidification. V-ATPase acidifies synaptic vesicles; F subunit would be present as part of the complex in neurons. Reason: Synaptic vesicle acidification is a non-core context for this ubiquitous subunit; primary function is lysosomal/organellar acidification. |
| GO:0000139 Golgi membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. V-ATPase acidifies the Golgi; F subunit is part of the complex. Reason: Well-established V-ATPase location in Golgi for glycosylation pathway function. |
| GO:0005765 lysosomal membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Lysosomal membrane is the primary functional location. Reason: Core localization. |
| GO:0005886 plasma membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | KEEP AS NON CORE | Summary: NAS from V-ATPase review. V-ATPase is targeted to plasma membrane in specialized cell types. Reason: Plasma membrane localization is real in specialized contexts but non-core for this ubiquitous subunit. |
| GO:0007035 vacuolar acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Core function of V-ATPase. Reason: Vacuolar acidification is the core biological process. |
| GO:0007042 lysosomal lumen acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. More specific than vacuolar acidification. Reason: Core function of V-ATPase. |
| GO:0007042 lysosomal lumen acidification | NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | ACCEPT | Summary: NAS from the structural study. Consistent. Reason: Core function. |
| GO:0010008 endosome membrane | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. V-ATPase acidifies endosomes. Reason: Endosome membrane is an established V-ATPase location. |
| GO:0016020 membrane | IDA PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | MARK AS OVER ANNOTATED | Summary: IDA from the cryo-EM study. F subunit is associated with membrane as part of the V-ATPase complex. Reason: Generic membrane annotation subsumed by more specific lysosomal/Golgi/endosome membrane annotations. |
| GO:0033176 proton-transporting V-type ATPase complex | NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | ACCEPT | Summary: NAS from the structural study. Consistent with IDA annotation from PMID:18752060. Reason: Core complex membership. |
| GO:0048388 endosomal lumen acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Endosomal lumen acidification is a core function. Reason: Core V-ATPase function. |
| GO:0051452 intracellular pH reduction | NAS PMID:32001091 Structure and Roles of V-type ATPases. | MARK AS OVER ANNOTATED | Summary: NAS from V-ATPase review. Generic term for the acidification function. Reason: Less specific than the individual lumen acidification terms; redundant and subsumed by more precise annotations. |
| GO:0061795 Golgi lumen acidification | NAS PMID:32001091 Structure and Roles of V-type ATPases. | ACCEPT | Summary: NAS from V-ATPase review. Golgi lumen acidification is important for glycosylation. Reason: Core V-ATPase function in Golgi. |
| GO:1902600 proton transmembrane transport | NAS PMID:33065002 Structures of a Complete Human V-ATPase Reveal Mechanisms of... | ACCEPT | Summary: NAS from the structural study. Reason: Core biological process. |
| GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain | ISS GO_REF:0000024 | ACCEPT | Summary: Ortholog-based annotation for V1 domain membership. Confirmed by cryo-EM structural data. Reason: Core structural membership of V1 domain confirmed by PMID:33065002. Supporting Evidence: PMID:33065002 Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. |
| GO:0042625 ATPase-coupled ion transmembrane transporter activity | NAS PMID:8581736 Cloning, sequencing and expression of a novel cDNA encoding ... | ACCEPT | Summary: NAS from the original cloning paper (Fujiwara et al. 1995). ATP6V1F is a component of an ATPase-coupled ion transporter complex. Reason: The ATPase-coupled ion transmembrane transporter activity is an appropriate molecular function annotation for a V-ATPase subunit. Supporting Evidence: PMID:8581736 A cDNA encoding the 14-kDa subunit of vacuolar ATPase was cloned from human fetal brain. The sequence was composed of 680 nucleotides containing an open reading frame of 357 nucleotides. |
| GO:0070062 extracellular exosome | HDA PMID:19199708 Proteomic analysis of human parotid gland exosomes by multid... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomics detection in parotid gland exosomes. Likely reflects membrane co-purification. Reason: Exosome detection is likely artifactual; not informative for core function. |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | MARK AS OVER ANNOTATED | Summary: High-throughput proteomics detection in urinary exosomes. Reason: Same reasoning as parotid exosome; likely artifactual. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-1222516 | KEEP AS NON CORE | Summary: Reactome TAS annotation. V1 F subunit can be in cytosol during regulated V1-V0 disassembly. Reason: The V1 domain including F subunit can exist as a soluble complex in cytosol. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-5252133 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-74723 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-917841 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9639286 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640167 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640168 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640175 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9640195 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9645598 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9645608 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9646468 | KEEP AS NON CORE | Summary: Reactome TAS annotation for cytosol. Reason: Consistent. |
| GO:0005515 protein binding | IPI PMID:18752060 The d subunit plays a central role in human vacuolar H(+)-AT... | MARK AS OVER ANNOTATED | Summary: The specific interaction underlying this annotation is the F subunit-V0 d subunit (ATP6V0D1) interaction, which is mechanistically central to the rotary pump mechanism. However, generic protein binding is not informative. Reason: Generic protein binding is uninformative; the specific D-F and F-d interactions are the mechanistically meaningful interaction, but no specific GO term captures this subunit-rotor interaction. Supporting Evidence: PMID:18752060 each can pull down the central stalk's D and F subunits from human kidney membrane, and in vitro studies using D and F further showed that the interactions between these proteins and the d subunit is direct. |
| GO:0016020 membrane | IDA PMID:18752060 The d subunit plays a central role in human vacuolar H(+)-AT... | MARK AS OVER ANNOTATED | Summary: IDA from Smith et al. (2008) showing F subunit in membrane preparations. Reason: Generic membrane is subsumed by more specific lysosomal/Golgi/endosome membrane annotations. |
| GO:0016471 vacuolar proton-transporting V-type ATPase complex | IDA PMID:18752060 The d subunit plays a central role in human vacuolar H(+)-AT... | ACCEPT | Summary: IDA from Smith et al. (2008) demonstrating F subunit co-purification with the V-ATPase complex. Direct biochemical evidence for complex membership. Reason: Direct experimental evidence for V-ATPase complex membership. This is the core complex membership annotation. Supporting Evidence: PMID:18752060 each can pull down the central stalk's D and F subunits from human kidney membrane, and in vitro studies using D and F further showed that the interactions between these proteins and the d subunit is direct. |
| GO:0015078 proton transmembrane transporter activity | NAS PMID:8581736 Cloning, sequencing and expression of a novel cDNA encoding ... | ACCEPT | Summary: NAS from the original cloning paper. Reason: Appropriate molecular function for a V-ATPase subunit. |
| GO:1902600 proton transmembrane transport | NAS PMID:8581736 Cloning, sequencing and expression of a novel cDNA encoding ... | ACCEPT | Summary: NAS from the original cloning paper. Reason: Core biological process of V-ATPase. Supporting Evidence: PMID:8581736 A cDNA encoding the 14-kDa subunit of vacuolar ATPase was cloned from human fetal brain. The sequence was composed of 680 nucleotides containing an open reading frame of 357 nucleotides. |
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Download this section (compressed HTML)Q: What is the precise structural role of the F subunit in coordinating the DF central rotor with both the A3B3 head and the V0 d subunit at the rotor-stator junction?
Q: Are there post-translational modifications on subunit F that regulate V-ATPase assembly or activity, particularly in response to nutrient availability?
Q: Do the two alternatively spliced isoforms of ATP6V1F differ in their incorporation into the V-ATPase complex or in their subcellular targeting?
Experiment: Cryo-EM analysis of V-ATPase in multiple rotational states at higher resolution to define the precise contacts between F subunit and the V0 d subunit at different stages of the catalytic cycle.
Hypothesis: The F subunit makes distinct contacts with V0 d subunit at different stages of the rotary catalytic cycle.
Type: structural biology
Experiment: Identification of post-translational modifications on the F subunit using quantitative mass spectrometry under varying nutrient conditions to assess regulation of V-ATPase activity.
Hypothesis: Post-translational modifications on the F subunit regulate V-ATPase assembly or activity.
Type: quantitative mass spectrometry
Experiment: CRISPR-based isoform knockout combined with rescue experiments using individual isoforms to determine whether either isoform has a distinct functional role in V-ATPase biology.
Hypothesis: ATP6V1F isoforms differ in V-ATPase incorporation or subcellular function.
Type: CRISPR functional genomics
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