ATP11

UniProt ID: P32453
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
Aliases:
YNL315C ATP synthase mitochondrial F1 complex assembly factor 1
📝 Provide Detailed Feedback

Gene Description

ATP11 encodes a mitochondrial matrix assembly factor for the F1 sector of mitochondrial F1FO ATP synthase. Atp11 is not a stoichiometric ATP synthase subunit; it is a dedicated assembly chaperone/stabilizing factor for the unassembled F1 beta subunit Atp2, preventing nonproductive aggregation and promoting formation of the alpha3-beta3 catalytic F1 head. Generic unfolded-protein binding and cross-species protein-binding annotations are less informative than the ATP synthase complex assembly and protein-containing complex stabilizing activity annotations.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005739 mitochondrion
IBA
GO_REF:0000033
ACCEPT
Summary: IBA mitochondrial localization is consistent with direct ATP11 localization.
Reason: Atp11 functions in mitochondria, specifically the matrix.
Supporting Evidence:
PMID:1532796
vitro import assays of ATP11 precursor and immunochemical evidence indicate that...the protein is located in mitochondria.
file:interpro/panther/PTHR13126/PTHR13126-metadata.yaml
PTHR13126 is the CHAPERONE ATP11 family.
GO:0140777 protein-containing complex stabilizing activity
IBA
GO_REF:0000033
ACCEPT
Summary: This is the most specific molecular-function term for Atp11.
Reason: Atp11 stabilizes the unassembled F1 beta subunit during ATP synthase assembly.
Supporting Evidence:
PMID:10681564
evidence that Atp11p binds selectively to the beta-subunit of F(1).
PMID:12829692
Atp11p yields a subfragment of the protein (called Atp11pTRNC) that retains...molecular chaperone function...the natural substrate (F1 beta).
file:yeast/ATP11/ATP11-deep-research-falcon.md
Atp11 binds F1 beta subunit Atp2 to prevent nonproductive self-association.
GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly
IBA
GO_REF:0000033
ACCEPT
Summary: The IBA process term matches classic ATP11 mutant and biochemical evidence.
Reason: ATP synthase F1 assembly is the central process affected by ATP11.
Supporting Evidence:
PMID:2142305
explanation for the mutant phenotype is a block in the assembly of the F1...oligomer.
PMID:36596815
it cooperates with the assembly...factors Atp11 and Atp12 to form the F1 domain of the ATP synthase.
GO:0005739 mitochondrion
IEA
GO_REF:0000120
ACCEPT
Summary: Electronic mitochondrion annotation is correct.
Reason: Atp11 is a mitochondrial matrix assembly factor.
Supporting Evidence:
PMID:1532796
The hybrid protein is detected in mitochondria with antibodies
GO:0065003 protein-containing complex assembly
IEA
GO_REF:0000002
MODIFY
Summary: The term is correct but too broad.
Reason: Replace with the specific mitochondrial ATP synthase assembly term.
Supporting Evidence:
PMID:2142305
important function at a...late stage in the synthesis of F1
GO:0005515 protein binding
IPI
PMID:27107014
An inter-species protein-protein interaction network across ...
REMOVE
Summary: This comes from a yeast-human inter-species interaction map and is not a physiological ATP11 function.
Reason: The annotation does not identify the endogenous yeast Atp2/F1 beta client and uses an uninformative term.
Supporting Evidence:
PMID:27107014
we generated a high-quality proteome-wide inter-interactome network map
GO:0005759 mitochondrial matrix
IDA
PMID:1532796
Characterization of ATP11 and detection of the encoded prote...
ACCEPT
Summary: Direct evidence supports mitochondrial matrix localization.
Reason: The F1 ATP synthase assembly role occurs in the matrix; PMID:1532796 detects Atp11 in mitochondria and reports co-purification with F1 alpha and beta subunits, which makes the matrix inference explicit.
Supporting Evidence:
PMID:1532796
Biotinated ATP11 protein can be partially...purified by affinity chromatography
PMID:1532796
biotinated ATP11 protein also contains the alpha and beta subunits of F1-ATPase
GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly
IMP
PMID:36596815
The mitochondrial Hsp70 controls the assembly of the F(1)F(O...
ACCEPT
Summary: Recent work places Atp11 with Atp12 and mtHsp70 in F1 assembly.
Reason: This is the specific ATP synthase assembly process affected by Atp11.
Supporting Evidence:
PMID:36596815
it cooperates with the assembly...factors Atp11 and Atp12 to form the F1 domain of the ATP synthase.
GO:0005739 mitochondrion
HDA
PMID:24769239
Quantitative variations of the mitochondrial proteome and ph...
ACCEPT
Summary: High-throughput mitochondrial proteomics is consistent with ATP11 biology.
Reason: Mitochondrial localization is core to Atp11 function.
Supporting Evidence:
PMID:24769239
isolated mitochondria extracted from yeast grown on fermentative...and respiratory...media
GO:0005739 mitochondrion
HDA
PMID:16823961
Toward the complete yeast mitochondrial proteome: multidimen...
ACCEPT
Summary: High-throughput mitochondrial proteome data are consistent with direct localization.
Reason: The broad mitochondrion term is correct.
Supporting Evidence:
PMID:16823961
A total of 851 different proteins (PROMITO dataset) were...identified by use of multidimensional LC-MS/MS
GO:0051082 unfolded protein binding
IDA
PMID:10681564
The assembly factor Atp11p binds to the beta-subunit of the ...
MODIFY
Summary: Atp11 binds an unassembled F1 beta subunit, but the generic term is too broad.
Reason: Protein-containing complex stabilizing activity better captures client-specific F1 assembly.
Supporting Evidence:
PMID:10681564
Atp11p bound to a region of the nucleotide-binding...domain of the beta-subunit
GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly
IPI
PMID:10681564
The assembly factor Atp11p binds to the beta-subunit of the ...
ACCEPT
Summary: The Atp11-F1 beta interaction directly supports ATP synthase F1 assembly.
Reason: This is the correct process-level interpretation of the Atp11-Atp2 interaction.
Supporting Evidence:
PMID:10681564
alpha-subunits may exchange for bound Atp11p...during the process of F(1) assembly.
GO:0005739 mitochondrion
IDA
PMID:1532796
Characterization of ATP11 and detection of the encoded prote...
ACCEPT
Summary: Direct evidence places Atp11 in mitochondria.
Reason: Mitochondrial localization is required for ATP synthase F1 assembly.
Supporting Evidence:
PMID:1532796
vitro import assays of ATP11 precursor and immunochemical evidence indicate that...the protein is located in mitochondria.
GO:0007005 mitochondrion organization
IMP
PMID:2142305
Identification of two nuclear genes (ATP11, ATP12) required ...
MODIFY
Summary: This broad phenotype should be replaced by the specific F1 ATP synthase assembly defect.
Reason: ATP11 mutants block F1 assembly, not general mitochondrial organization as a primary function.
Supporting Evidence:
PMID:2142305
important function at a...late stage in the synthesis of F1
GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly
IMP
PMID:2142305
Identification of two nuclear genes (ATP11, ATP12) required ...
ACCEPT
Summary: Classic genetic evidence directly supports ATP synthase assembly.
Reason: ATP11 was identified as required for assembly of yeast F1-ATPase.
Supporting Evidence:
PMID:2142305
explanation for the mutant phenotype is a block in the assembly of the F1...oligomer.
GO:0051082 unfolded protein binding
IDA
PMID:12829692
A purified subfragment of yeast Atp11p retains full molecula...
MODIFY
Summary: Atp11 has chaperone activity toward F1 beta, but the term is too generic.
Reason: GO:0140777 better represents stabilization of an ATP synthase assembly intermediate.
Supporting Evidence:
PMID:12829692
Atp11p yields a subfragment of the protein (called Atp11pTRNC) that retains...molecular chaperone function...the natural substrate (F1 beta).

Core Functions

Dedicated mitochondrial F1 ATP synthase assembly chaperone/stabilizing activity. Atp11 binds unassembled F1 beta subunit Atp2 in the mitochondrial matrix, preventing nonproductive aggregation and promoting assembly of the alpha3-beta3 F1 catalytic head.

Supporting Evidence:
  • PMID:10681564
    evidence that Atp11p binds selectively to the beta-subunit of F(1).
  • PMID:12829692
    Atp11p yields a subfragment of the protein (called Atp11pTRNC) that retains...molecular chaperone function...the natural substrate (F1 beta).
  • file:yeast/ATP11/ATP11-deep-research-falcon.md
    ATP11 encodes a mitochondrial ATP synthase-specific assembly chaperone for F1 beta subunit Atp2.

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Combined Automated Annotation using Multiple IEA Methods
Characterization of ATP11 and detection of the encoded protein in mitochondria of Saccharomyces cerevisiae.
  • ATP11 protein is mitochondrial
    "In vitro import assays and immunochemical evidence indicate mitochondrial localization."
Identification of two nuclear genes (ATP11, ATP12) required for assembly of the yeast F1-ATPase.
  • ATP11 is required for F1 ATPase assembly
    "Mutations in ATP11 and ATP12 block a late step in F1 assembly."
The assembly factor Atp11p binds to the beta-subunit of the mitochondrial F(1)-ATPase.
  • Atp11 binds the F1 beta subunit during assembly
    "Atp11p binds selectively to the beta-subunit of F1."
A purified subfragment of yeast Atp11p retains full molecular chaperone activity.
  • Atp11 has chaperone activity with F1 beta as its natural substrate
    "Atp11pTRNC retains molecular chaperone function with the natural substrate F1 beta."
Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.
Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae.
An inter-species protein-protein interaction network across vast evolutionary distance.
The mitochondrial Hsp70 controls the assembly of the F(1)F(O)-ATP synthase.
  • mtHsp70 cooperates with Atp11 and Atp12 in F1 assembly
    "Mitochondrial Hsp70 cooperates with the assembly factors Atp11 and Atp12 to form the F1 domain."
file:yeast/ATP11/ATP11-deep-research-falcon.md
Falcon deep research report for ATP11
  • ATP11 is a mitochondrial F1 ATP synthase assembly chaperone
    "Atp11 binds F1 beta subunit Atp2 and promotes formation of the F1 catalytic head."
file:interpro/panther/PTHR13126/PTHR13126-metadata.yaml
PANTHER family metadata for ATP11 family PTHR13126
  • PTHR13126 is the ATP11 chaperone family
    "The local PANTHER metadata identifies PTHR13126 as CHAPERONE ATP11."

Suggested Questions for Experts

Q: Should experimental GO:0051082 annotations for ATP11 be replaced by GO:0140777 to reflect client-specific stabilization of F1 ATP synthase assembly intermediates?

📚 Additional Documentation

Deep Research Falcon

(ATP11-deep-research-falcon.md)

provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T10:45:28.740458'
end_time: '2026-05-04T10:57:35.549715'
duration_seconds: 726.81
template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: ATP11
gene_symbol: ATP11
uniprot_accession: P32453
protein_description: 'RecName: Full=Protein ATP11, mitochondrial; Flags: Precursor;'
gene_info: Name=ATP11; OrderedLocusNames=YNL315C; ORFNames=N0357;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the ATP11 family. .
protein_domains: ATP11. (IPR010591); ATP11 (PF06644)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 31


Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P32453
  • Protein Description: RecName: Full=Protein ATP11, mitochondrial; Flags: Precursor;
  • Gene Information: Name=ATP11; OrderedLocusNames=YNL315C; ORFNames=N0357;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the ATP11 family. .
  • Key Domains: ATP11. (IPR010591); ATP11 (PF06644)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "ATP11" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'ATP11' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene ATP11 (gene ID: ATP11, UniProt: P32453) in yeast.

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.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P32453
  • Protein Description: RecName: Full=Protein ATP11, mitochondrial; Flags: Precursor;
  • Gene Information: Name=ATP11; OrderedLocusNames=YNL315C; ORFNames=N0357;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the ATP11 family. .
  • Key Domains: ATP11. (IPR010591); ATP11 (PF06644)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "ATP11" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'ATP11' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene ATP11 (gene ID: ATP11, UniProt: P32453) in yeast.

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.

Research report: ATP11 (YNL315C; UniProt P32453) in Saccharomyces cerevisiae

Executive summary

ATP11 (YNL315C; UniProt P32453) encodes Atp11p, a mitochondrial-matrix, ATP-synthase–specific assembly chaperone that binds the F1 β subunit (Atp2) to prevent its nonproductive self-association and to promote formation of the F1 catalytic head (α3β3 hexamer) of mitochondrial F1FO-ATP synthase (Complex V). Atp11p is not a stoichiometric subunit of the mature enzyme but is required for efficient respiratory growth and correct mitochondrial ultrastructure; loss of ATP11 leads to α/β inclusion bodies in the matrix and impaired oxidative phosphorylation. Newer work (2023) adds mitochondrial Hsp70 as a cooperating factor with Atp11/Atp12 in F1 assembly and quality control. (franco2020modularassemblyof pages 7-10, hinton2003apurifiedsubfragment pages 1-2, lefebvrelegendre2005failuretoassemble pages 1-2, ludlam2009chaperonesoff1atpase pages 1-2, song2023themitochondrialhsp70 pages 1-2)


1) Key concepts and definitions (current understanding)

1.1 What “ATP11” means in yeast (identity verification)

In S. cerevisiae, ATP11 (YNL315C) encodes Atp11p, a dedicated chaperone/assembly factor required for biogenesis of the F1 sector of mitochondrial ATP synthase. Its function is specific to ATP synthase assembly rather than broad protein import/folding, and it acts on unassembled F1 subunits in the matrix. (potocka2007assemblyfactorsin pages 17-21, franco2020modularassemblyof pages 7-10)

1.2 ATP synthase (Complex V) biogenesis and where ATP11 fits

Mitochondrial F1FO-ATP synthase is built from modular subassemblies. The F1 module (soluble catalytic head in the matrix) contains an α3β3 hexamer with the catalytic and noncatalytic nucleotide-binding interfaces. Dedicated assembly chaperones Atp11 and Atp12 bind newly imported F1 subunits to prevent aggregation and ensure productive oligomerization before integration with the stalk and FO membrane sector. (franco2020modularassemblyof pages 7-10, song2018assemblingthemitochondrial pages 1-2)

1.3 Assembly chaperone vs. enzyme: “substrate specificity” for ATP11

Atp11p is not an enzyme with a chemical substrate; its “substrate specificity” is client-protein specificity. The key client is the F1 β subunit, which Atp11p binds transiently during assembly. This binding prevents β from forming nonproductive complexes and promotes correct αβ interactions leading to the (αβ)3 hexamer. (hinton2003apurifiedsubfragment pages 1-2, ludlam2009chaperonesoff1atpase pages 1-2)


2) Molecular function, mechanism, and pathway placement (evidence-based)

2.1 Molecular function: a β-subunit assembly chaperone

Multiple experimental approaches support a direct Atp11p–β interaction: affinity tag pull-down and yeast two-hybrid assays showed Atp11p binds free/unassembled F1 β, and mechanistic interpretation is that Atp11p binding shields aggregation-prone surfaces to prevent β–β self-association and to facilitate productive formation of the (αβ)3 hexamer. (hinton2003apurifiedsubfragment pages 1-2, potocka2007assemblyfactorsin pages 17-21)

A structured chaperone-active truncation (removal of 67 N-terminal residues) retains chaperone activity in vitro (e.g., suppressing aggregation of reduced insulin B chain) and retains interaction with the natural F1 β client, indicating that a large portion of Atp11p’s functional chaperone surface resides outside the N-terminus. (hinton2003apurifiedsubfragment pages 1-2)

2.2 Binding interface and mechanistic models for chaperone release

Review synthesis and interaction mapping indicate Atp11p and Atp12p bind ~200-residue regions within nucleotide-binding domains of β and α, respectively, consistent with a model in which these assembly factors prevent premature α–β interface formation until appropriate assembly progression. (potocka2007assemblyfactorsin pages 17-21)

Earlier mechanistic models posited that the chaperones might resemble α/β; however, structural studies argue Atp11p/Atp12p do not mimic α or β. Instead, assembly progression involves release of the chaperones triggered by association of the γ subunit (central stalk), enabling maturation of the F1 hexamer. (ludlam2009chaperonesoff1atpase pages 1-2)

2.3 Pathway placement relative to general mitochondrial folding systems (Hsp60/Hsp70)

Atp11p is described as acting downstream of general chaperones (e.g., Hsp60/Hsp70) because atp11 mutants accumulate near-mature α and β subunits (processed/imported) but fail to assemble them, leading to aggregation rather than precursor accumulation—contrasting with general folding/import defects. (potocka2007assemblyfactorsin pages 17-21, franco2020modularassemblyof pages 7-10)


3) Subcellular localization and where the function occurs

Atp11p functions in the mitochondrial matrix, where the F1 catalytic head is assembled and where unassembled α and β subunits can otherwise aggregate. Mitochondrial targeting is supported by the use of leader peptides in constructs and by the matrix-localized phenotypes (matrix inclusion bodies). (hinton2003apurifiedsubfragment pages 1-2, ludlam2009chaperonesoff1atpase pages 3-4, lefebvrelegendre2005failuretoassemble pages 1-2)


4) Phenotypes, statistics, and quantitative data from experimental studies

4.1 Respiratory growth phenotypes

Loss of ATP11 impairs oxidative phosphorylation capacity and growth on nonfermentable carbon sources; in comparative phenotyping, atp11Δ can display a “leaky” respiratory phenotype, whereas atp12Δ can be fully defective on ethanol/glycerol (EG) medium under tested conditions. (ludlam2009chaperonesoff1atpase pages 3-4)

4.2 Inclusion bodies and mitochondrial ultrastructure (quantitative EM)

A key experimental signature of ATP11 loss is formation of electron-dense mitochondrial inclusion bodies enriched in F1 α/β proteins. In quantitative ultrastructural analysis, Δatp11 displayed inclusion bodies in 44.0% of cell sections and 23.5% of mitochondrial profiles, consistent with a strong block in α3β3 subcomplex assembly. (lefebvrelegendre2005failuretoassemble pages 1-2, lefebvrelegendre2005failuretoassemble media b3ecdee8)

These inclusion bodies are supported by EM and immunolabeling evidence and correlate with mitochondrial structural defects (including cristae abnormalities) when F1 assembly fails. (lefebvrelegendre2005failuretoassemble pages 1-2, lefebvrelegendre2005failuretoassemble media 33a6c4d5, lefebvrelegendre2005failuretoassemble media 5e421669)


5) Recent developments and latest research (prioritizing 2023–2024)

5.1 2023: mtHsp70 cooperates with Atp11/Atp12 and adds quality control

A 2023 Nature Communications study identified a dual role for mitochondrial Hsp70 (mtHsp70) in ATP synthase biogenesis: it (i) cooperates with Atp11 and Atp12 to form the F1 domain, and (ii) transfers Atp5/OSCP into the assembly line to connect the catalytic head to the peripheral stalk. Importantly, mtHsp70 inactivation permits incorporation of assembly-defective Atp5 variants into mature complexes, implying a quality-control checkpoint during ATP synthase assembly. (song2023themitochondrialhsp70 pages 1-2)

This reframes ATP11 action as part of a broader chaperone network: a specialized, client-specific assembly chaperone (Atp11) works alongside a general mitochondrial chaperone (mtHsp70) to coordinate formation and linkage of the F1 head. (song2023themitochondrialhsp70 pages 1-2)

5.2 2024: cross-species/clinical synthesis of ATP11 homolog ATPAF1

A 2024 systematic review of isolated ATP synthase defects explicitly identifies ATPAF1 as the human homolog of yeast ATP11, describing it as conserved and required for α3β3 hexamer formation. In the compiled variant landscape for isolated ATP synthase deficiency (total variants n = 63), ~60% (38/63) are nuclear-encoded; ATPAF1 is listed with 0 reported pathogenic variants in that review’s assembly-factor table, while other assembly factors (e.g., TMEM70) account for many cases. (tauchmannova2024variabilityofclinical pages 3-5)

While this is not a yeast functional discovery per se, it underscores ATP11’s mechanistic importance and conservation, and it motivates yeast ATP11 studies as models for fundamental assembly biology relevant to mitochondrial disease mechanisms. (tauchmannova2024variabilityofclinical pages 3-5, tauchmannova2024variabilityofclinical pages 1-3)


6) Current applications and real-world implementations

6.1 Yeast ATP11 as a mechanistic model system

ATP11 is widely used as a genetic and biochemical handle to:
- induce specific blocks in F1 assembly (yielding clean assembly intermediates/inclusion bodies),
- study the coupling of chaperone systems to respiratory complex biogenesis,
- and test cross-species complementation or structure–function relationships of ATP11-family proteins.

For example, structural/functional work showed that C. glabrata Atp11p can complement S. cerevisiae atp11Δ respiratory defects, supporting conserved chaperone function and enabling structure-informed mutational analysis. (ludlam2009chaperonesoff1atpase pages 3-4, ludlam2009chaperonesoff1atpase pages 4-5)

6.2 Structural biology of assembly factors

Atp11-family proteins have been purified and structurally characterized to inform mechanistic models of client binding and chaperone release during F1 assembly. Structural mapping also highlighted specific residues whose mutation inactivates Atp11p function, supporting a surface-mediated chaperone mechanism rather than catalytic chemistry. (ludlam2009chaperonesoff1atpase pages 4-5)


7) Expert opinions and analysis (authoritative syntheses)

7.1 Consensus view

Across reviews and primary literature, the consensus is that ATP11 encodes a specialized assembly chaperone for mitochondrial ATP synthase that:
- binds β (Atp2),
- prevents α/β aggregation,
- promotes (αβ)3 hexamer formation,
- and is released during later assembly steps (γ involvement),
while general chaperones (Hsp60/Hsp70) support upstream folding/import. (franco2020modularassemblyof pages 7-10, ludlam2009chaperonesoff1atpase pages 1-2, song2018assemblingthemitochondrial pages 1-2)

7.2 Conservation across genomes

Comparative-genomics analyses support conservation of Atp11p/Atp12p function across eukaryotes capable of oxidative phosphorylation, consistent with a conserved need to protect α/β subunits during assembly. (pickova2005assemblyfactorsof pages 1-2)


Evidence map (table)

Claim/Topic Key evidence/data System/assay Primary source
Molecular function ATP11/YNL315C encodes Atp11p, a dedicated mitochondrial F1-ATPase assembly chaperone rather than a stoichiometric ATP synthase subunit; it prevents nonproductive self-association/aggregation of unassembled F1 subunits and promotes formation of the catalytic (αβ)3 hexamer (franco2020modularassemblyof pages 7-10, hinton2003apurifiedsubfragment pages 1-2, ludlam2009chaperonesoff1atpase pages 1-2) Yeast genetics, biochemical assembly analysis, in vitro chaperone assays Hinton et al. 2003, J Biol Chem (2003-09), https://doi.org/10.1074/jbc.M305353200; Ludlam et al. 2009, J Biol Chem (2009-06), https://doi.org/10.1074/jbc.M109.002568
Localization Atp11p is a soluble mitochondrial matrix protein/assembly factor acting on the matrix-exposed F1 sector during ATP synthase biogenesis; it is imported with a mitochondrial targeting sequence and is not part of the final holoenzyme (hinton2003apurifiedsubfragment pages 1-2, ludlam2009chaperonesoff1atpase pages 3-4, song2018assemblingthemitochondrial pages 1-2) Mitochondrial targeting constructs, mitochondrial biochemical studies, review synthesis Hinton et al. 2003, J Biol Chem (2003-09), https://doi.org/10.1074/jbc.M305353200; Ludlam et al. 2009, J Biol Chem (2009-06), https://doi.org/10.1074/jbc.M109.002568; Song et al. 2018, PNAS (2018-03), https://doi.org/10.1073/pnas.1801697115
Binding partner/client specificity Atp11p specifically binds the F1 β subunit (Atp2), whereas Atp12p binds F1 α (Atp1); interaction evidence comes from affinity pull-down/coprecipitation and yeast two-hybrid studies, and binding maps to regions in the nucleotide-binding domain of β (potocka2007assemblyfactorsin pages 17-21, hinton2003apurifiedsubfragment pages 1-2, ludlam2009chaperonesoff1atpase pages 1-2) Affinity-tag pull-down, co-precipitation, yeast two-hybrid, interaction mapping Hinton et al. 2003, J Biol Chem (2003-09), https://doi.org/10.1074/jbc.M305353200; Ludlam et al. 2009, J Biol Chem (2009-06), https://doi.org/10.1074/jbc.M109.002568
Mutant phenotype atp11Δ mutants are respiratory deficient or strongly impaired for growth on nonfermentable carbon sources; α and β subunits accumulate as large insoluble aggregates/inclusion bodies in the mitochondrial matrix instead of assembling into F1, with reduced ATPase/oxidative phosphorylation capacity (potocka2007assemblyfactorsin pages 17-21, lefebvrelegendre2005failuretoassemble pages 1-2, ludlam2009chaperonesoff1atpase pages 1-2, lefebvrelegendre2001identificationofa pages 6-7) Yeast gene deletion, respiratory growth assays, mitochondrial fractionation, EM Lefebvre-Legendre et al. 2005, J Biol Chem (2005-05), https://doi.org/10.1074/jbc.M410789200; Lefebvre-Legendre et al. 2001, J Biol Chem (2001-03), https://doi.org/10.1074/jbc.M009557200
Quantitative phenotype/statistics Electron microscopy quantified inclusion bodies in Δatp11: 44.0% of cell sections and 23.5% of mitochondrial profiles contained inclusion bodies, supporting a severe block in α3β3 subcomplex assembly (lefebvrelegendre2005failuretoassemble pages 1-2, lefebvrelegendre2005failuretoassemble media b3ecdee8) Electron microscopy, immunogold labeling, quantitative ultrastructural scoring Lefebvre-Legendre et al. 2005, J Biol Chem (2005-05), https://doi.org/10.1074/jbc.M410789200
Mechanistic model Atp11p and Atp12p protect β and α, respectively, from premature α-β contacts; early models proposed they occupy catalytic/noncatalytic interface regions, while later structural work argued the chaperones do not mimic α/β and that F1 γ-subunit association helps trigger chaperone release during hexamer assembly (franco2020modularassemblyof pages 7-10, ludlam2009chaperonesoff1atpase pages 1-2, song2018assemblingthemitochondrial pages 1-2) Structural biology, interaction assays, mechanistic modeling, review synthesis Ludlam et al. 2009, J Biol Chem (2009-06), https://doi.org/10.1074/jbc.M109.002568; Song et al. 2018, PNAS (2018-03), https://doi.org/10.1073/pnas.1801697115; Franco et al. 2020, Biological Chemistry (2020-05), https://doi.org/10.1515/hsz-2020-0112
Relationship to broader ATP synthase pathway F1 assembly depends on upstream folding assistance and downstream incorporation into modular ATP synthase assembly; Hsp60 assists β folding before Atp11 action, and properly assembled F1 is coupled to later steps in ATP synthase biogenesis and translational feedback on mitochondrially encoded subunits (franco2020modularassemblyof pages 7-10, song2018assemblingthemitochondrial pages 1-2) Review synthesis of genetic/biochemical pathway studies Franco et al. 2020, Biological Chemistry (2020-05), https://doi.org/10.1515/hsz-2020-0112; Song et al. 2018, PNAS (2018-03), https://doi.org/10.1073/pnas.1801697115
Recent 2023 developments A 2023 study added mtHsp70 as an active participant in ATP synthase biogenesis: mtHsp70 cooperates with Atp11/Atp12 in F1 assembly, transfers Atp5/OSCP into the assembly line, and exerts quality control by preventing defective Atp5 variants from being inappropriately incorporated into mature complexes (song2023themitochondrialhsp70 pages 1-2) Yeast proteomics, pull-downs, mutant analysis, assembly-state profiling Song et al. 2023, Nature Communications (2023-01), https://doi.org/10.1038/s41467-022-35720-5
Expert/current understanding Recent authoritative reviews continue to define ATP11 as a conserved F1 assembly factor/chaperone (human ortholog ATPAF1), with core function centered on β-subunit handling during ATP synthase biogenesis; direct 2023-2024 ATP11-specific yeast primary studies remain limited, so new insight comes mainly from broader assembly-network work rather than redefinition of ATP11’s core role (franco2020modularassemblyof pages 7-10, song2023themitochondrialhsp70 pages 1-2) Review analysis and recent mechanistic study Franco et al. 2020, Biological Chemistry (2020-05), https://doi.org/10.1515/hsz-2020-0112; Song et al. 2023, Nature Communications (2023-01), https://doi.org/10.1038/s41467-022-35720-5

Table: This table summarizes the main experimentally supported findings for Saccharomyces cerevisiae ATP11/YNL315C, including function, localization, binding specificity, mutant phenotypes, mechanistic models, and recent 2023 developments. It is useful as a compact evidence map linking each major claim to the assay type and primary literature source.


URLs and publication dates (key sources used)

  • Hinton A, Zuiderweg ERP, Ackerman SH. 2003-09. J Biol Chem. “A Purified Subfragment of Yeast Atp11p Retains Full Molecular Chaperone Activity.” https://doi.org/10.1074/jbc.M305353200 (hinton2003apurifiedsubfragment pages 1-2)
  • Lefebvre-Legendre L et al. 2005-05. J Biol Chem. “Failure to Assemble the α3β3 Subcomplex…” https://doi.org/10.1074/jbc.M410789200 (lefebvrelegendre2005failuretoassemble pages 1-2)
  • Ludlam A et al. 2009-06. J Biol Chem. “Chaperones of F1-ATPase.” https://doi.org/10.1074/jbc.M109.002568 (ludlam2009chaperonesoff1atpase pages 1-2)
  • Song J, Pfanner N, Becker T. 2018-03. PNAS. “Assembling the mitochondrial ATP synthase.” https://doi.org/10.1073/pnas.1801697115 (song2018assemblingthemitochondrial pages 1-2)
  • Franco LVR, Su CH, Tzagoloff A. 2020-05. Biological Chemistry. “Modular assembly of yeast mitochondrial ATP synthase…” https://doi.org/10.1515/hsz-2020-0112 (franco2020modularassemblyof pages 7-10)
  • Song J et al. 2023-01. Nature Communications. “The mitochondrial Hsp70 controls the assembly of the F1FO-ATP synthase.” https://doi.org/10.1038/s41467-022-35720-5 (song2023themitochondrialhsp70 pages 1-2)
  • Tauchmannová K et al. 2024-08. Physiological Research. “Variability of Clinical Phenotypes Caused by Isolated Defects of Mitochondrial ATP Synthase.” https://doi.org/10.33549/physiolres.935407 (tauchmannova2024variabilityofclinical pages 3-5)

Limitations / evidence gaps

Direct ATP11-focused yeast primary studies in 2023–2024 are limited in the retrieved corpus; the newest mechanistic advance relevant to ATP11 here is primarily the integration of Atp11/Atp12 into an mtHsp70-mediated assembly and quality-control framework. (song2023themitochondrialhsp70 pages 1-2)

References

  1. (franco2020modularassemblyof pages 7-10): Leticia Veloso Ribeiro Franco, Chen Hsien Su, and Alexander Tzagoloff. Modular assembly of yeast mitochondrial atp synthase and cytochrome oxidase. Biological Chemistry, 401:835-853, May 2020. URL: https://doi.org/10.1515/hsz-2020-0112, doi:10.1515/hsz-2020-0112. This article has 35 citations and is from a peer-reviewed journal.

  2. (hinton2003apurifiedsubfragment pages 1-2): Ayana Hinton, Erik R.P. Zuiderweg, and Sharon H. Ackerman. A purified subfragment of yeast atp11p retains full molecular chaperone activity*. Journal of Biological Chemistry, 278:34110-34113, Sep 2003. URL: https://doi.org/10.1074/jbc.m305353200, doi:10.1074/jbc.m305353200. This article has 10 citations and is from a domain leading peer-reviewed journal.

  3. (lefebvrelegendre2005failuretoassemble pages 1-2): Linnka Lefebvre-Legendre, Bénédicte Salin, Jacques Schaëffer, Daniel Brèthes, Alain Dautant, Sharon H. Ackerman, and Jean-Paul di Rago. Failure to assemble the α3 β3 subcomplex of the atp synthase leads to accumulation of the α and β subunits within inclusion bodies and the loss of mitochondrial cristae in saccharomyces cerevisiae*. Journal of Biological Chemistry, 280:18386-18392, May 2005. URL: https://doi.org/10.1074/jbc.m410789200, doi:10.1074/jbc.m410789200. This article has 83 citations and is from a domain leading peer-reviewed journal.

  4. (ludlam2009chaperonesoff1atpase pages 1-2): Anthony Ludlam, Joseph Brunzelle, Thomas Pribyl, Xingjue Xu, Domenico L. Gatti, and Sharon H. Ackerman. Chaperones of f1-atpase. Journal of Biological Chemistry, 284:17138-17146, Jun 2009. URL: https://doi.org/10.1074/jbc.m109.002568, doi:10.1074/jbc.m109.002568. This article has 40 citations and is from a domain leading peer-reviewed journal.

  5. (song2023themitochondrialhsp70 pages 1-2): Jiyao Song, Liesa Steidle, Isabelle Steymans, Jasjot Singh, Anne Sanner, Lena Böttinger, Dominic Winter, and Thomas Becker. The mitochondrial hsp70 controls the assembly of the f1fo-atp synthase. Nature Communications, Jan 2023. URL: https://doi.org/10.1038/s41467-022-35720-5, doi:10.1038/s41467-022-35720-5. This article has 26 citations and is from a highest quality peer-reviewed journal.

  6. (potocka2007assemblyfactorsin pages 17-21): A Potocká. Assembly factors in the biogenesis of mitochondrial atp synthase. Unknown journal, 2007.

  7. (song2018assemblingthemitochondrial pages 1-2): Jiyao Song, Nikolaus Pfanner, and Thomas Becker. Assembling the mitochondrial atp synthase. Proceedings of the National Academy of Sciences, 115:2850-2852, Mar 2018. URL: https://doi.org/10.1073/pnas.1801697115, doi:10.1073/pnas.1801697115. This article has 84 citations and is from a highest quality peer-reviewed journal.

  8. (ludlam2009chaperonesoff1atpase pages 3-4): Anthony Ludlam, Joseph Brunzelle, Thomas Pribyl, Xingjue Xu, Domenico L. Gatti, and Sharon H. Ackerman. Chaperones of f1-atpase. Journal of Biological Chemistry, 284:17138-17146, Jun 2009. URL: https://doi.org/10.1074/jbc.m109.002568, doi:10.1074/jbc.m109.002568. This article has 40 citations and is from a domain leading peer-reviewed journal.

  9. (lefebvrelegendre2005failuretoassemble media b3ecdee8): Linnka Lefebvre-Legendre, Bénédicte Salin, Jacques Schaëffer, Daniel Brèthes, Alain Dautant, Sharon H. Ackerman, and Jean-Paul di Rago. Failure to assemble the α3 β3 subcomplex of the atp synthase leads to accumulation of the α and β subunits within inclusion bodies and the loss of mitochondrial cristae in saccharomyces cerevisiae*. Journal of Biological Chemistry, 280:18386-18392, May 2005. URL: https://doi.org/10.1074/jbc.m410789200, doi:10.1074/jbc.m410789200. This article has 83 citations and is from a domain leading peer-reviewed journal.

  10. (lefebvrelegendre2005failuretoassemble media 33a6c4d5): Linnka Lefebvre-Legendre, Bénédicte Salin, Jacques Schaëffer, Daniel Brèthes, Alain Dautant, Sharon H. Ackerman, and Jean-Paul di Rago. Failure to assemble the α3 β3 subcomplex of the atp synthase leads to accumulation of the α and β subunits within inclusion bodies and the loss of mitochondrial cristae in saccharomyces cerevisiae*. Journal of Biological Chemistry, 280:18386-18392, May 2005. URL: https://doi.org/10.1074/jbc.m410789200, doi:10.1074/jbc.m410789200. This article has 83 citations and is from a domain leading peer-reviewed journal.

  11. (lefebvrelegendre2005failuretoassemble media 5e421669): Linnka Lefebvre-Legendre, Bénédicte Salin, Jacques Schaëffer, Daniel Brèthes, Alain Dautant, Sharon H. Ackerman, and Jean-Paul di Rago. Failure to assemble the α3 β3 subcomplex of the atp synthase leads to accumulation of the α and β subunits within inclusion bodies and the loss of mitochondrial cristae in saccharomyces cerevisiae*. Journal of Biological Chemistry, 280:18386-18392, May 2005. URL: https://doi.org/10.1074/jbc.m410789200, doi:10.1074/jbc.m410789200. This article has 83 citations and is from a domain leading peer-reviewed journal.

  12. (tauchmannova2024variabilityofclinical pages 3-5): K. Tauchmannová, A. Pecinová, J. Houštěk, and T. Mrázek. Variability of clinical phenotypes caused by isolated defects of mitochondrial atp synthase. Physiological Research, pages S243-S278, Aug 2024. URL: https://doi.org/10.33549/physiolres.935407, doi:10.33549/physiolres.935407. This article has 14 citations and is from a peer-reviewed journal.

  13. (tauchmannova2024variabilityofclinical pages 1-3): K. Tauchmannová, A. Pecinová, J. Houštěk, and T. Mrázek. Variability of clinical phenotypes caused by isolated defects of mitochondrial atp synthase. Physiological Research, pages S243-S278, Aug 2024. URL: https://doi.org/10.33549/physiolres.935407, doi:10.33549/physiolres.935407. This article has 14 citations and is from a peer-reviewed journal.

  14. (ludlam2009chaperonesoff1atpase pages 4-5): Anthony Ludlam, Joseph Brunzelle, Thomas Pribyl, Xingjue Xu, Domenico L. Gatti, and Sharon H. Ackerman. Chaperones of f1-atpase. Journal of Biological Chemistry, 284:17138-17146, Jun 2009. URL: https://doi.org/10.1074/jbc.m109.002568, doi:10.1074/jbc.m109.002568. This article has 40 citations and is from a domain leading peer-reviewed journal.

  15. (pickova2005assemblyfactorsof pages 1-2): Andrea Pícková, Martin Potocký, and Josef Houštěk. Assembly factors of f1fo‐atp synthase across genomes. Proteins: Structure, 59:393-402, May 2005. URL: https://doi.org/10.1002/prot.20452, doi:10.1002/prot.20452. This article has 43 citations.

  16. (lefebvrelegendre2001identificationofa pages 6-7): Linnka Lefebvre-Legendre, Jacques Vaillier, Houssain Benabdelhak, Jean Velours, Piotr P. Slonimski, and Jean-Paul di Rago. Identification of a nuclear gene (fmc1) required for the assembly/stability of yeast mitochondrial f1-atpase in heat stress conditions*. The Journal of Biological Chemistry, 276:6789-6796, Mar 2001. URL: https://doi.org/10.1074/jbc.m009557200, doi:10.1074/jbc.m009557200. This article has 179 citations.

Citations

  1. hinton2003apurifiedsubfragment pages 1-2
  2. potocka2007assemblyfactorsin pages 17-21
  3. tauchmannova2024variabilityofclinical pages 3-5
  4. pickova2005assemblyfactorsof pages 1-2
  5. lefebvrelegendre2005failuretoassemble pages 1-2
  6. song2018assemblingthemitochondrial pages 1-2
  7. franco2020modularassemblyof pages 7-10
  8. tauchmannova2024variabilityofclinical pages 1-3
  9. lefebvrelegendre2001identificationofa pages 6-7
  10. https://doi.org/10.1074/jbc.M305353200;
  11. https://doi.org/10.1074/jbc.M109.002568
  12. https://doi.org/10.1074/jbc.M109.002568;
  13. https://doi.org/10.1073/pnas.1801697115
  14. https://doi.org/10.1074/jbc.M410789200;
  15. https://doi.org/10.1074/jbc.M009557200
  16. https://doi.org/10.1074/jbc.M410789200
  17. https://doi.org/10.1073/pnas.1801697115;
  18. https://doi.org/10.1515/hsz-2020-0112
  19. https://doi.org/10.1515/hsz-2020-0112;
  20. https://doi.org/10.1038/s41467-022-35720-5
  21. https://doi.org/10.1074/jbc.M305353200
  22. https://doi.org/10.33549/physiolres.935407
  23. https://doi.org/10.1515/hsz-2020-0112,
  24. https://doi.org/10.1074/jbc.m305353200,
  25. https://doi.org/10.1074/jbc.m410789200,
  26. https://doi.org/10.1074/jbc.m109.002568,
  27. https://doi.org/10.1038/s41467-022-35720-5,
  28. https://doi.org/10.1073/pnas.1801697115,
  29. https://doi.org/10.33549/physiolres.935407,
  30. https://doi.org/10.1002/prot.20452,
  31. https://doi.org/10.1074/jbc.m009557200,

📄 View Raw YAML

id: P32453
gene_symbol: ATP11
product_type: PROTEIN
status: COMPLETE
aliases:
- YNL315C
- ATP synthase mitochondrial F1 complex assembly factor 1
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  ATP11 encodes a mitochondrial matrix assembly factor for the F1 sector of
  mitochondrial F1FO ATP synthase. Atp11 is not a stoichiometric ATP synthase
  subunit; it is a dedicated assembly chaperone/stabilizing factor for the
  unassembled F1 beta subunit Atp2, preventing nonproductive aggregation and
  promoting formation of the alpha3-beta3 catalytic F1 head. Generic
  unfolded-protein binding and cross-species protein-binding annotations are less
  informative than the ATP synthase complex assembly and protein-containing
  complex stabilizing activity annotations.
existing_annotations:
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA mitochondrial localization is consistent with direct ATP11 localization.
    action: ACCEPT
    reason: Atp11 functions in mitochondria, specifically the matrix.
    supported_by:
    - reference_id: PMID:1532796
      supporting_text: vitro import assays of ATP11 precursor and immunochemical evidence indicate that...the protein is located in mitochondria.
    - reference_id: file:interpro/panther/PTHR13126/PTHR13126-metadata.yaml
      supporting_text: PTHR13126 is the CHAPERONE ATP11 family.
- term:
    id: GO:0140777
    label: protein-containing complex stabilizing activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: This is the most specific molecular-function term for Atp11.
    action: ACCEPT
    reason: Atp11 stabilizes the unassembled F1 beta subunit during ATP synthase assembly.
    supported_by:
    - reference_id: PMID:10681564
      supporting_text: evidence that Atp11p binds selectively to the beta-subunit of F(1).
    - reference_id: PMID:12829692
      supporting_text: Atp11p yields a subfragment of the protein (called Atp11pTRNC) that retains...molecular chaperone function...the natural substrate (F1 beta).
    - reference_id: file:yeast/ATP11/ATP11-deep-research-falcon.md
      supporting_text: Atp11 binds F1 beta subunit Atp2 to prevent nonproductive self-association.
- term:
    id: GO:0033615
    label: mitochondrial proton-transporting ATP synthase complex assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: The IBA process term matches classic ATP11 mutant and biochemical evidence.
    action: ACCEPT
    reason: ATP synthase F1 assembly is the central process affected by ATP11.
    supported_by:
    - reference_id: PMID:2142305
      supporting_text: explanation for the mutant phenotype is a block in the assembly of the F1...oligomer.
    - reference_id: PMID:36596815
      supporting_text: it cooperates with the assembly...factors Atp11 and Atp12 to form the F1 domain of the ATP synthase.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Electronic mitochondrion annotation is correct.
    action: ACCEPT
    reason: Atp11 is a mitochondrial matrix assembly factor.
    supported_by:
    - reference_id: PMID:1532796
      supporting_text: The hybrid protein is detected in mitochondria with antibodies
- term:
    id: GO:0065003
    label: protein-containing complex assembly
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: The term is correct but too broad.
    action: MODIFY
    reason: Replace with the specific mitochondrial ATP synthase assembly term.
    proposed_replacement_terms:
    - id: GO:0033615
      label: mitochondrial proton-transporting ATP synthase complex assembly
    supported_by:
    - reference_id: PMID:2142305
      supporting_text: important function at a...late stage in the synthesis of F1
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27107014
  review:
    summary: This comes from a yeast-human inter-species interaction map and is not a physiological ATP11 function.
    action: REMOVE
    reason: The annotation does not identify the endogenous yeast Atp2/F1 beta client and uses an uninformative term.
    supported_by:
    - reference_id: PMID:27107014
      supporting_text: we generated a high-quality proteome-wide inter-interactome network map
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IDA
  original_reference_id: PMID:1532796
  review:
    summary: Direct evidence supports mitochondrial matrix localization.
    action: ACCEPT
    reason: The F1 ATP synthase assembly role occurs in the matrix; PMID:1532796 detects Atp11 in mitochondria and reports co-purification with F1 alpha and beta subunits, which makes the matrix inference explicit.
    supported_by:
    - reference_id: PMID:1532796
      supporting_text: Biotinated ATP11 protein can be partially...purified by affinity chromatography
    - reference_id: PMID:1532796
      supporting_text: biotinated ATP11 protein also contains the alpha and beta subunits of F1-ATPase
- term:
    id: GO:0033615
    label: mitochondrial proton-transporting ATP synthase complex assembly
  evidence_type: IMP
  original_reference_id: PMID:36596815
  review:
    summary: Recent work places Atp11 with Atp12 and mtHsp70 in F1 assembly.
    action: ACCEPT
    reason: This is the specific ATP synthase assembly process affected by Atp11.
    supported_by:
    - reference_id: PMID:36596815
      supporting_text: it cooperates with the assembly...factors Atp11 and Atp12 to form the F1 domain of the ATP synthase.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HDA
  original_reference_id: PMID:24769239
  review:
    summary: High-throughput mitochondrial proteomics is consistent with ATP11 biology.
    action: ACCEPT
    reason: Mitochondrial localization is core to Atp11 function.
    supported_by:
    - reference_id: PMID:24769239
      supporting_text: isolated mitochondria extracted from yeast grown on fermentative...and respiratory...media
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HDA
  original_reference_id: PMID:16823961
  review:
    summary: High-throughput mitochondrial proteome data are consistent with direct localization.
    action: ACCEPT
    reason: The broad mitochondrion term is correct.
    supported_by:
    - reference_id: PMID:16823961
      supporting_text: A total of 851 different proteins (PROMITO dataset) were...identified by use of multidimensional LC-MS/MS
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:10681564
  review:
    summary: Atp11 binds an unassembled F1 beta subunit, but the generic term is too broad.
    action: MODIFY
    reason: Protein-containing complex stabilizing activity better captures client-specific F1 assembly.
    proposed_replacement_terms:
    - id: GO:0140777
      label: protein-containing complex stabilizing activity
    supported_by:
    - reference_id: PMID:10681564
      supporting_text: Atp11p bound to a region of the nucleotide-binding...domain of the beta-subunit
- term:
    id: GO:0033615
    label: mitochondrial proton-transporting ATP synthase complex assembly
  evidence_type: IPI
  original_reference_id: PMID:10681564
  review:
    summary: The Atp11-F1 beta interaction directly supports ATP synthase F1 assembly.
    action: ACCEPT
    reason: This is the correct process-level interpretation of the Atp11-Atp2 interaction.
    supported_by:
    - reference_id: PMID:10681564
      supporting_text: alpha-subunits may exchange for bound Atp11p...during the process of F(1) assembly.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:1532796
  review:
    summary: Direct evidence places Atp11 in mitochondria.
    action: ACCEPT
    reason: Mitochondrial localization is required for ATP synthase F1 assembly.
    supported_by:
    - reference_id: PMID:1532796
      supporting_text: vitro import assays of ATP11 precursor and immunochemical evidence indicate that...the protein is located in mitochondria.
- term:
    id: GO:0007005
    label: mitochondrion organization
  evidence_type: IMP
  original_reference_id: PMID:2142305
  review:
    summary: This broad phenotype should be replaced by the specific F1 ATP synthase assembly defect.
    action: MODIFY
    reason: ATP11 mutants block F1 assembly, not general mitochondrial organization as a primary function.
    proposed_replacement_terms:
    - id: GO:0033615
      label: mitochondrial proton-transporting ATP synthase complex assembly
    supported_by:
    - reference_id: PMID:2142305
      supporting_text: important function at a...late stage in the synthesis of F1
- term:
    id: GO:0033615
    label: mitochondrial proton-transporting ATP synthase complex assembly
  evidence_type: IMP
  original_reference_id: PMID:2142305
  review:
    summary: Classic genetic evidence directly supports ATP synthase assembly.
    action: ACCEPT
    reason: ATP11 was identified as required for assembly of yeast F1-ATPase.
    supported_by:
    - reference_id: PMID:2142305
      supporting_text: explanation for the mutant phenotype is a block in the assembly of the F1...oligomer.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:12829692
  review:
    summary: Atp11 has chaperone activity toward F1 beta, but the term is too generic.
    action: MODIFY
    reason: GO:0140777 better represents stabilization of an ATP synthase assembly intermediate.
    proposed_replacement_terms:
    - id: GO:0140777
      label: protein-containing complex stabilizing activity
    supported_by:
    - reference_id: PMID:12829692
      supporting_text: Atp11p yields a subfragment of the protein (called Atp11pTRNC) that retains...molecular chaperone function...the natural substrate (F1 beta).
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:1532796
  title: Characterization of ATP11 and detection of the encoded protein in mitochondria of Saccharomyces cerevisiae.
  findings:
  - statement: ATP11 protein is mitochondrial
    supporting_text: In vitro import assays and immunochemical evidence indicate mitochondrial localization.
- id: PMID:2142305
  title: Identification of two nuclear genes (ATP11, ATP12) required for assembly of the yeast F1-ATPase.
  findings:
  - statement: ATP11 is required for F1 ATPase assembly
    supporting_text: Mutations in ATP11 and ATP12 block a late step in F1 assembly.
- id: PMID:10681564
  title: The assembly factor Atp11p binds to the beta-subunit of the mitochondrial F(1)-ATPase.
  findings:
  - statement: Atp11 binds the F1 beta subunit during assembly
    supporting_text: Atp11p binds selectively to the beta-subunit of F1.
- id: PMID:12829692
  title: A purified subfragment of yeast Atp11p retains full molecular chaperone activity.
  findings:
  - statement: Atp11 has chaperone activity with F1 beta as its natural substrate
    supporting_text: Atp11pTRNC retains molecular chaperone function with the natural substrate F1 beta.
- id: PMID:16823961
  title: 'Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.'
  findings: []
- id: PMID:24769239
  title: Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae.
  findings: []
- id: PMID:27107014
  title: An inter-species protein-protein interaction network across vast evolutionary distance.
  findings: []
- id: PMID:36596815
  title: The mitochondrial Hsp70 controls the assembly of the F(1)F(O)-ATP synthase.
  findings:
  - statement: mtHsp70 cooperates with Atp11 and Atp12 in F1 assembly
    supporting_text: Mitochondrial Hsp70 cooperates with the assembly factors Atp11 and Atp12 to form the F1 domain.
- id: file:yeast/ATP11/ATP11-deep-research-falcon.md
  title: Falcon deep research report for ATP11
  findings:
  - statement: ATP11 is a mitochondrial F1 ATP synthase assembly chaperone
    supporting_text: Atp11 binds F1 beta subunit Atp2 and promotes formation of the F1 catalytic head.
- id: file:interpro/panther/PTHR13126/PTHR13126-metadata.yaml
  title: PANTHER family metadata for ATP11 family PTHR13126
  findings:
  - statement: PTHR13126 is the ATP11 chaperone family
    supporting_text: The local PANTHER metadata identifies PTHR13126 as CHAPERONE ATP11.
core_functions:
- description: >-
    Dedicated mitochondrial F1 ATP synthase assembly chaperone/stabilizing
    activity. Atp11 binds unassembled F1 beta subunit Atp2 in the mitochondrial
    matrix, preventing nonproductive aggregation and promoting assembly of the
    alpha3-beta3 F1 catalytic head.
  molecular_function:
    id: GO:0140777
    label: protein-containing complex stabilizing activity
  directly_involved_in:
  - id: GO:0033615
    label: mitochondrial proton-transporting ATP synthase complex assembly
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  - id: GO:0005739
    label: mitochondrion
  supported_by:
  - reference_id: PMID:10681564
    supporting_text: evidence that Atp11p binds selectively to the beta-subunit of F(1).
  - reference_id: PMID:12829692
    supporting_text: Atp11p yields a subfragment of the protein (called Atp11pTRNC) that retains...molecular chaperone function...the natural substrate (F1 beta).
  - reference_id: file:yeast/ATP11/ATP11-deep-research-falcon.md
    supporting_text: ATP11 encodes a mitochondrial ATP synthase-specific assembly chaperone for F1 beta subunit Atp2.
proposed_new_terms: []
suggested_questions:
- question: Should experimental GO:0051082 annotations for ATP11 be replaced by GO:0140777 to reflect client-specific stabilization of F1 ATP synthase assembly intermediates?
suggested_experiments: []