ATP5IF1

id: Q9UII2
gene_symbol: ATP5IF1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  ATP5IF1 (also known as IF1 or ATPIF1) encodes the mitochondrial ATPase inhibitor,
  a small nuclear-encoded protein that reversibly inhibits the F1Fo-ATP synthase
  (complex V) to prevent wasteful ATP hydrolysis when the mitochondrial membrane
  potential collapses (e.g., during ischemia or hypoxia). IF1 is active as an
  antiparallel dimer at acidic pH (<6.7) and inactive as a tetramer at neutral pH.
  The N-terminal inhibitory region (residues 26-52) binds the alpha/beta catalytic
  interface of the F1 domain and contacts the gamma subunit to block rotary
  catalysis. IF1 also binds the OSCP subunit, which protects cancer cells from
  permeability transition pore-dependent apoptosis. Phosphorylation at Ser39 by
  a mitochondrial PKA-like activity inactivates IF1. The protein is overexpressed
  in many cancers and contributes to the glycolytic Warburg phenotype. IF1 also
  indirectly regulates heme synthesis in erythroid tissues and promotes ATP synthase
  dimerization, which influences cristae morphology.
alternative_products:
- name: '1'
  id: Q9UII2-1
- name: '2'
  id: Q9UII2-2
  sequence_note: VSP_041417
- name: '3'
  id: Q9UII2-3
  sequence_note: VSP_041418
existing_annotations:
# ============================================================
# IBA (phylogenetic inference) annotations
# ============================================================
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for cytoplasm based on phylogenetic inference. While IF1 is
      primarily a mitochondrial matrix protein, the precursor form is synthesized
      in the cytoplasm before import. The IBA also includes plant orthologs (TAIR
      locus) and bovine P01096, suggesting broad conservation. However, cytoplasm
      is a very general CC term and the primary active localization of IF1 is
      mitochondrial.
    action: REMOVE
    reason: >-
      The GOA qualifier is is_active_in, and the available evidence supports
      cytosolic synthesis/import transit rather than ATP5IF1 being active in
      cytoplasm. The functional location of IF1 is mitochondrial, especially the
      matrix-facing F1Fo-ATP synthase context.
    supported_by:
      - reference_id: PMID:10664857
        supporting_text: "cDNA coding the human homolog of the inhibitor protein was isolated and sequenced"

- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for mitochondrion based on phylogenetic inference across
      the ATPase inhibitor family. This is the primary active localization of IF1.
    action: ACCEPT
    reason: >-
      Mitochondrial localization is the core cellular compartment for IF1. The
      mature protein functions in the mitochondrial matrix where it binds the F1
      catalytic domain of ATP synthase. This is supported by multiple experimental
      studies (PMID:12110673, PMID:35926043) and UniProt annotation.
    supported_by:
      - reference_id: PMID:12110673
        supporting_text: "IF(1) could be co-isolated with F(1)F(0) when the immunocapture procedure was carried out at pH 6.5 but was absent when the ATP synthase was isolated at pH 8.0"

- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for heme biosynthetic process based on phylogenetic inference
      from mouse (MGI:1196457) and zebrafish (ZFIN:ZDB-GENE-070410-36) orthologs.
      Shah et al. (2012, PMID:23135403) demonstrated that Atpif1 regulates heme
      synthesis in developing erythroblasts by modulating mitochondrial pH and
      redox potential, allowing FECH to catalyze iron incorporation into
      protoporphyrin IX.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a genuine but indirect role of IF1. The protein does not directly
      participate in heme biosynthetic enzymology; rather, by inhibiting ATP
      hydrolysis, IF1 maintains mitochondrial pH and redox conditions favorable
      for FECH activity. UniProt explicitly states: "Indirectly acts as a
      regulator of heme synthesis in erythroid tissues: regulates heme synthesis
      by modulating the mitochondrial pH and redox potential, allowing FECH to
      efficiently catalyze the incorporation of iron into protoporphyrin IX to
      produce heme" (PMID:23135403). This is a secondary consequence of its
      primary ATPase inhibitor activity, relevant mainly in erythroid tissues.
    supported_by:
      - reference_id: PMID:23135403
        supporting_text: "Mitochondrial Atpif1 regulates haem synthesis in developing erythroblasts"

- term:
    id: GO:0030218
    label: erythrocyte differentiation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for erythrocyte differentiation based on phylogenetic
      inference from mouse and zebrafish orthologs. The evidence comes from
      PMID:23135403 showing that Atpif1 is required for proper heme synthesis
      during erythroid development.
    action: KEEP_AS_NON_CORE
    reason: >-
      Like heme biosynthesis, erythrocyte differentiation is an indirect
      downstream consequence of IF1's ATPase inhibitor activity. IF1 is not
      an erythroid-specific transcription factor or signaling molecule; it
      supports erythropoiesis by maintaining mitochondrial conditions needed
      for heme synthesis. This represents a tissue-specific pleiotropic effect
      rather than a core molecular function.
    supported_by:
      - reference_id: PMID:23135403
        supporting_text: "Mitochondrial Atpif1 regulates haem synthesis in developing erythroblasts"

- term:
    id: GO:0042030
    label: ATPase inhibitor activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for ATPase inhibitor activity based on phylogenetic inference
      across the ATPase inhibitor family (bovine P01096, rat RGD:2181, and human
      Q9UII2). This is the defining molecular function of IF1.
    action: ACCEPT
    reason: >-
      ATPase inhibitor activity is the core molecular function of ATP5IF1. The
      protein is named for this activity and belongs to the ATPase inhibitor
      family. IF1 inhibits the ATP hydrolase activity of F1Fo-ATP synthase,
      preventing wasteful ATP consumption when the proton gradient collapses
      (PMID:12110673, PMID:15528193, PMID:24005319). The IBA correctly reflects
      the conserved function across mammals.
    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"
      - reference_id: PMID:15528193
        supporting_text: "IF1 protein bound to purified F(1) ATP synthase and inhibited F(1)-dependent ATP hydrolysis consistent with its reported activity in studies of mitochondria"
      - reference_id: file:human/ATP5IF1/ATP5IF1-deep-research-falcon.md
        supporting_text: "IF1 is a reversible, pH-sensitive inhibitor that primarily prevents wasteful ATP hydrolysis when Δψm collapses, but can also inhibit ATP synthesis in some contexts"

- term:
    id: GO:0051117
    label: ATPase binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for ATPase binding based on phylogenetic inference. IF1
      physically binds the F1 catalytic domain of ATP synthase, contacting the
      alpha/beta subunit interface and the gamma subunit.
    action: ACCEPT
    reason: >-
      ATPase binding is a core function that underlies the inhibitory activity
      of IF1. Structural and biochemical studies demonstrate direct binding to
      the F1 domain. The IBA annotation is consistent with the well-established
      mechanism of IF1 action. Aggeler et al. (PMID:12110673) showed IF1
      co-isolates with F1Fo at pH 6.5, and UniProt documents the binding
      interface at the alpha-beta subunit interface (residues 26-52).
    supported_by:
      - reference_id: PMID:12110673
        supporting_text: "IF(1) could be co-isolated with F(1)F(0) when the immunocapture procedure was carried out at pH 6.5"

# ============================================================
# IEA (electronic annotation) annotations
# ============================================================
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for mitochondrion based on combined automated methods
      including InterPro domain (IPR007648) and UniProt subcellular location
      annotation. Consistent with all other evidence for mitochondrial localization.
    action: ACCEPT
    reason: >-
      This electronic annotation is consistent with the well-established
      mitochondrial localization of IF1, supported by multiple experimental
      evidence codes (IDA, HTP, HDA, ISS, TAS, IBA). The InterPro domain
      IPR007648 (ATPase_inhibitor_mt) is specifically a mitochondrial domain.

- term:
    id: GO:0042030
    label: ATPase inhibitor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA annotation for ATPase inhibitor activity based on InterPro domain
      IPR007648 mapping. This is the defining function of the protein family.
    action: ACCEPT
    reason: >-
      The InterPro-based electronic annotation correctly identifies the core
      molecular function. The ATPase_inhibitor_mt domain (IPR007648) is
      directly associated with ATPase inhibitor activity, and this is the
      primary function of IF1 supported by extensive experimental evidence.

# ============================================================
# Protein binding IPI annotations (high-throughput interactome studies)
# ============================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  review:
    summary: >-
      IPI annotation for protein binding from the BioPlex 2.0 human interactome
      study (Huttlin et al. 2017). The WITH column indicates binding to P06576
      (ATP5F1B, the beta subunit of F1-ATP synthase). This interaction is
      biologically meaningful and well-established.
    action: MODIFY
    reason: >-
      While the interaction with ATP5F1B (beta subunit) is real and reflects
      the core mechanism of IF1, "protein binding" (GO:0005515) is uninformative.
      The specific interaction with the beta subunit of ATP synthase is the
      mechanistic basis of IF1's inhibitory function. A more specific term
      should be used.
    proposed_replacement_terms:
      - id: GO:0140260
        label: mitochondrial proton-transporting ATP synthase complex binding
    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 annotation for protein binding from a crosslinking mass spectrometry
      study of intact cell nuclei (Fasci et al. 2018). The WITH column indicates
      binding to P06576 (ATP5F1B). This study focused on histone interactions
      in nuclei, making ATP5IF1 detection likely a contaminant or crossreactive
      hit.
    action: REMOVE
    reason: >-
      This intact-nuclei XL-MS study does not provide reliable support for a
      physiological mitochondrial ATP5IF1-ATP5F1B interaction. The core ATP synthase
      complex binding function is already supported by direct mitochondrial evidence
      from other publications, so this nuclear-context protein-binding row should
      not be modified into that term.
    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:32296183
  review:
    summary: >-
      IPI annotation for protein binding from the HuRI reference binary
      interactome map (Luck et al. 2020). The WITH column indicates binding
      to Q9HAQ2 (KIF9) and Q9NRD5 (PICK1). These are high-throughput Y2H
      hits with no clear biological relevance to IF1's known function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      KIF9 and PICK1 are not known to have any functional relationship with
      mitochondrial ATP synthase or IF1's inhibitory activity. These likely
      represent false-positive or non-physiological interactions from
      high-throughput Y2H screening. The generic "protein binding" term
      combined with HTP interactome partners of unclear relevance makes
      this an over-annotation.
    supported_by:
      - reference_id: PMID:32296183
        supporting_text: "A reference map of the human binary protein interactome"

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32807793
  review:
    summary: >-
      IPI annotation for protein binding from Sharanek et al. 2020, studying
      mitochondrial OSMR in glioblastoma. The WITH column indicates binding to
      Q99650 (OSMR). The paper found OSMR localizes to mitochondria and
      interacts with complex I, and IF1 was detected as an interactor.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While OSMR was shown to localize to mitochondria, the interaction with
      IF1 is likely an indirect association within the mitochondrial inner
      membrane protein network rather than a direct functional interaction.
      The paper focuses on OSMR-complex I interactions, not IF1. The generic
      "protein binding" term does not capture any meaningful functional
      relationship.
    supported_by:
      - reference_id: PMID:32807793
        supporting_text: "OSMR controls glioma stem cell respiration and confers resistance of glioblastoma to ionizing radiation"

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32814053
  review:
    summary: >-
      IPI annotation for protein binding from a neurodegenerative disease
      interactome mapping study (Haenig et al. 2020). The WITH column lists
      many diverse proteins (PMP22, DMWD, NEFL, TOR1A, KLF11, DNAJB6, DNM2,
      FGFR3, GLE1, GRN, GSN, HRAS, A2M, ADRB2, MECP2, NUP58, SPRED1,
      P28329-3/CHAT, P28799-2/GRN). These represent high-throughput Y2H hits
      from a disease-focused interactome screen.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This is a large-scale interactome study focused on neurodegenerative
      disease proteins. The vast majority of these interactors (NEFL, MECP2,
      HRAS, FGFR3, GSN, A2M, etc.) have no plausible direct functional
      relationship with mitochondrial IF1. These are likely false positives
      or non-physiological interactions from Y2H. The sheer number and
      diversity of partners argues against specificity. "Protein binding"
      is already uninformative and these interactions do not add functional
      insight.
    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 annotation for protein binding from BioPlex 3.0 (Huttlin et al. 2021).
      The WITH column indicates binding to P06576 (ATP5F1B, beta subunit of
      F1-ATP synthase). This is the same core interaction as PMID:28514442.
    action: MODIFY
    reason: >-
      The interaction with ATP5F1B is the core functional binding partner of
      IF1 and is well-established. However, "protein binding" is uninformative.
      A more specific term should be used.
    proposed_replacement_terms:
      - id: GO:0140260
        label: mitochondrial proton-transporting ATP synthase complex binding
    supported_by:
      - reference_id: PMID:33961781
        supporting_text: "Dual proteome-scale networks reveal cell-specific remodeling of the human interactome"

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  review:
    summary: >-
      IPI annotation for protein binding from Schaffer et al. 2025 multimodal
      cell maps study. The WITH column indicates binding to P06576 (ATP5F1B).
      Again, the same core interaction with the beta subunit.
    action: MODIFY
    reason: >-
      Same rationale as for PMID:28514442 and PMID:33961781. The interaction
      with ATP5F1B is real but "protein binding" is uninformative. A more
      specific MF term exists.
    proposed_replacement_terms:
      - id: GO:0140260
        label: mitochondrial proton-transporting ATP synthase complex binding
    supported_by:
      - reference_id: PMID:40205054
        supporting_text: "Multimodal cell maps as a foundation for structural and functional genomics"

# ============================================================
# IEA annotations from Ensembl Compara
# ============================================================
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for heme biosynthetic process transferred from mouse
      ortholog O35143 via Ensembl Compara. Consistent with the IBA annotation
      and the experimental evidence from Shah et al. (PMID:23135403).
    action: KEEP_AS_NON_CORE
    reason: >-
      This electronic transfer from the mouse ortholog is consistent with
      the IBA annotation and PMID:23135403 showing IF1 regulates heme
      synthesis indirectly. Same rationale as the IBA annotation: this is
      a genuine but non-core function.

- term:
    id: GO:0030218
    label: erythrocyte differentiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation for erythrocyte differentiation transferred from mouse
      ortholog O35143 via Ensembl Compara. Consistent with the IBA annotation
      and PMID:23135403.
    action: KEEP_AS_NON_CORE
    reason: >-
      Same rationale as the IBA annotation for this term: erythrocyte
      differentiation is a tissue-specific downstream consequence of IF1's
      ATPase inhibitor activity supporting heme synthesis.

# ============================================================
# IMP (mutant phenotype) annotations from PMID:24005319
# ============================================================
- term:
    id: GO:0045732
    label: positive regulation of protein catabolic process
  evidence_type: IMP
  original_reference_id: PMID:24005319
  review:
    summary: >-
      IMP annotation from Lefebvre et al. 2013 genome-wide RNAi screen that
      identified ATPIF1 as essential for PARK2 recruitment and mitophagy. ATPIF1
      knockdown blocked PARK2-dependent ubiquitination and subsequent mitophagy
      of damaged mitochondria, which involves protein catabolism of
      ubiquitinated mitochondrial substrates.
    action: KEEP_AS_NON_CORE
    reason: >-
      The connection to protein catabolism is through the PINK1-PARK2 mitophagy
      pathway. ATPIF1 promotes mitochondrial depolarization during uncoupling,
      which triggers PARK2 recruitment and ubiquitination of mitochondrial
      proteins for proteasomal/autophagic degradation. This is an indirect
      downstream consequence of IF1's primary ATPase inhibitor activity.
      While experimentally demonstrated, it is not a core function.
    supported_by:
      - reference_id: PMID:24005319
        supporting_text: "we identified ATPase inhibitory factor 1 (ATPIF1/IF1) as essential for PARK2 recruitment and mitophagy in cultured cells"

- term:
    id: GO:1905707
    label: negative regulation of mitochondrial ATP synthesis coupled proton transport
  evidence_type: IMP
  original_reference_id: PMID:24005319
  review:
    summary: >-
      IMP annotation from Lefebvre et al. 2013 showing that ATPIF1 blocks
      ATP synthase from running in reverse (as an ATPase) during uncoupling.
      The annotation captures the process-level consequence of IF1's ATPase
      inhibitor activity on ATP synthesis coupled proton transport.
    action: ACCEPT
    reason: >-
      This annotation correctly captures the core biological process function
      of IF1. During mitochondrial uncoupling, the F1Fo-ATP synthase can
      reverse to hydrolyze ATP and pump protons. IF1 inhibits this reversal,
      effectively negatively regulating the overall ATP synthesis coupled
      proton transport process. Lefebvre et al. showed "ATPIF1 promotes
      collapse of delta-psi and activation of the PINK-PARK2 mitophagy
      pathway by blocking the ATPase activity of the F1-Fo ATP synthase"
      (PMID:24005319).
    supported_by:
      - reference_id: PMID:24005319
        supporting_text: "During uncoupling, ATPIF1 promotes collapse of ΔΨ and activation of the PINK-PARK2 mitophagy pathway by blocking the ATPase activity of the F 1-Fo ATP synthase"

# ============================================================
# IDA annotations from various sources
# ============================================================
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: >-
      IDA annotation for mitochondrion based on curation of immunofluorescence
      data (Human Protein Atlas). Direct visualization of IF1 in mitochondria.
    action: ACCEPT
    reason: >-
      Direct immunofluorescence evidence for mitochondrial localization is
      consistent with all other evidence. HPA data provides independent
      confirmation of the core localization.

- term:
    id: GO:0002931
    label: response to ischemia
  evidence_type: IDA
  original_reference_id: PMID:35926043
  review:
    summary: >-
      IDA annotation from Wyant et al. 2022 (Science) showing that ATPIF1 is
      involved in ischemic protection. GPR35 activation led to ATPIF1-dependent
      ATP synthase dimerization that prevented ATP loss during ischemia. The
      study demonstrated that "Activated GPR35, in an ATPIF1-dependent and
      pertussis toxin-sensitive manner, induced ATP synthase dimerization,
      which prevented ATP loss upon ischemia."
    action: KEEP_AS_NON_CORE
    reason: >-
      Response to ischemia is biologically important and experimentally
      demonstrated, but it represents a physiological context in which IF1's
      primary ATPase inhibitor function is deployed, rather than the core
      function itself. IF1's role in ischemic protection is a consequence
      of its ability to prevent ATP hydrolysis when the proton gradient
      collapses. This is a key physiological role but secondary to the
      molecular function.
    supported_by:
      - reference_id: PMID:35926043
        supporting_text: "Activated GPR35, in an ATPIF1-dependent and pertussis toxin-sensitive manner, induced ATP synthase dimerization, which prevented ATP loss upon ischemia"

- term:
    id: GO:0010667
    label: negative regulation of cardiac muscle cell apoptotic process
  evidence_type: IDA
  original_reference_id: PMID:35926043
  review:
    summary: >-
      IDA annotation from Wyant et al. 2022 showing that ATPIF1-dependent
      ATP synthase dimerization contributes to cardiac protection during
      ischemia. By preventing ATP depletion, IF1 protects cardiac cells
      from apoptosis during ischemic stress.
    action: UNDECIDED
    reason: >-
      The accessible evidence supports GPR35/ATPIF1-dependent ATP synthase
      dimerization and ATP preservation during ischemia, but the cached support
      does not directly establish negative regulation of cardiac muscle cell
      apoptosis. Treat this as undecided until direct apoptosis evidence from the
      paper is available.
    supported_by:
      - reference_id: PMID:35926043
        supporting_text: "Activated GPR35, in an ATPIF1-dependent and pertussis toxin-sensitive manner, induced ATP synthase dimerization, which prevented ATP loss upon ischemia"

# ============================================================
# TAS annotation for ATPase inhibitor activity
# ============================================================
- term:
    id: GO:0042030
    label: ATPase inhibitor activity
  evidence_type: TAS
  original_reference_id: PMID:24005319
  review:
    summary: >-
      TAS annotation for ATPase inhibitor activity based on Lefebvre et al.
      2013. The paper describes ATPIF1 as "blocking the ATPase activity of
      the F1-Fo ATP synthase" during uncoupling.
    action: ACCEPT
    reason: >-
      ATPase inhibitor activity is the core molecular function. This TAS
      annotation is consistent with all other evidence for this function.
      The paper explicitly describes ATPIF1 blocking ATPase activity.
    supported_by:
      - reference_id: PMID:24005319
        supporting_text: "During uncoupling, ATPIF1 promotes collapse of ΔΨ and activation of the PINK-PARK2 mitophagy pathway by blocking the ATPase activity of the F 1-Fo ATP synthase"

# ============================================================
# HTP annotation for mitochondrion
# ============================================================
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  review:
    summary: >-
      HTP annotation for mitochondrion from Morgenstern et al. 2021, a
      quantitative high-confidence human mitochondrial proteome study.
      ATP5IF1 was identified as a high-confidence mitochondrial protein.
    action: ACCEPT
    reason: >-
      This high-throughput proteomics study provides quantitative evidence
      for mitochondrial localization. Consistent with all other evidence
      codes for this localization.
    supported_by:
      - reference_id: PMID:34800366
        supporting_text: "Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context"

# ============================================================
# ISS annotations transferred from bovine ortholog P01096
# ============================================================
- term:
    id: GO:1905707
    label: negative regulation of mitochondrial ATP synthesis coupled proton transport
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation transferred from bovine ortholog P01096. The bovine IF1
      was the first characterized member of this family and shares high
      sequence conservation with human IF1. The function is well-conserved.
    action: ACCEPT
    reason: >-
      This ISS annotation is consistent with the IMP annotation from
      PMID:24005319 for the same GO term. The bovine ortholog is the
      best-studied member of this family, and the transfer is appropriate
      given high sequence conservation and shared function.

- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation indicating IF1 is part of a protein-containing complex,
      transferred from bovine ortholog P01096. IF1 forms homodimers and
      associates with the F1Fo-ATP synthase complex.
    action: REMOVE
    reason: >-
      While IF1 is indeed part of protein complexes (homodimers and the
      IF1-ATP synthase complex), "protein-containing complex" is too generic and
      there is no appropriate same-aspect CC replacement here. The relevant biology
      is already captured by more specific annotations: mitochondrial localization
      and the supported MF annotation for mitochondrial proton-transporting ATP
      synthase complex binding (GO:0140260).

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for identical protein binding (homodimerization)
      transferred from bovine ortholog P01096. IF1 forms antiparallel
      dimers at acidic pH, which is the active inhibitory form, and
      homotetramers at neutral pH, which is the inactive form.
    action: ACCEPT
    reason: >-
      Homodimerization is a critical regulatory mechanism for IF1.
      UniProt states: "Homodimer; represents the active form and is
      present at a pH value below 6.5. Homotetramer; represents the
      inactive form and is present at a pH value above 7.0." The
      antiparallel coiled-coil dimer (residues 74-106) is essential
      for the inhibitory mechanism. While "identical protein binding"
      is somewhat generic, it accurately captures the homodimerization
      property.
    supported_by:
      - reference_id: PMID:12110673
        supporting_text: "IF(1) could be co-isolated with F(1)F(0) when the immunocapture procedure was carried out at pH 6.5 but was absent when the ATP synthase was isolated at pH 8.0"

# ============================================================
# IDA for ATP synthase complex binding
# ============================================================
- term:
    id: GO:0140260
    label: mitochondrial proton-transporting ATP synthase complex binding
  evidence_type: IDA
  original_reference_id: PMID:12110673
  review:
    summary: >-
      IDA annotation for direct binding to the mitochondrial ATP synthase
      complex, from Aggeler et al. 2002. The study demonstrated
      co-immunoprecipitation of IF1 with F1Fo-ATP synthase from human
      heart mitochondria in a pH-dependent manner.
    action: ACCEPT
    reason: >-
      This is a core molecular function annotation. Aggeler et al. directly
      demonstrated that IF1 co-purifies with immunocaptured F1Fo-ATP synthase
      at pH 6.5 but not at pH 8.0, confirming direct pH-dependent binding.
      The captured complex could be inhibited >90% by recombinant IF1 and
      activated >10-fold by pH 8.0 release.
    supported_by:
      - reference_id: PMID:12110673
        supporting_text: "IF(1) could be co-isolated with F(1)F(0) when the immunocapture procedure was carried out at pH 6.5 but was absent when the ATP synthase was isolated at pH 8.0"
      - reference_id: PMID:12110673
        supporting_text: "Immunocaptured F(1)F(0) lacking IF(1) could be inhibited by more than 90% by addition of recombinant inhibitor protein"

# ============================================================
# IMP for mitophagy from PMID:24005319
# ============================================================
- term:
    id: GO:1905091
    label: positive regulation of type 2 mitophagy
  evidence_type: IMP
  original_reference_id: PMID:24005319
  review:
    summary: >-
      IMP annotation from Lefebvre et al. 2013 genome-wide RNAi screen.
      ATPIF1 was identified as essential for PARK2 recruitment to depolarized
      mitochondria and subsequent mitophagy. ATPIF1 promotes mitochondrial
      depolarization by blocking reverse ATP synthase activity, which is
      required for PINK1 stabilization and PARK2 recruitment.
    action: KEEP_AS_NON_CORE
    reason: >-
      Mitophagy regulation is an experimentally supported but indirect
      consequence of IF1's primary ATPase inhibitor activity. IF1 promotes
      mitophagy by ensuring complete mitochondrial depolarization during
      uncoupling (by preventing ATP hydrolysis-driven proton pumping),
      which allows PINK1 accumulation and PARK2 recruitment. This is a
      downstream biological process rather than a core function.
    supported_by:
      - reference_id: PMID:24005319
        supporting_text: "we identified ATPase inhibitory factor 1 (ATPIF1/IF1) as essential for PARK2 recruitment and mitophagy in cultured cells"
      - reference_id: PMID:24005319
        supporting_text: "Restoration of ATPIF1 in Rho0 cells, which lack mtDNA and a functional electron transport chain, lowers ΔΨ and triggers PARK2 recruitment"

# ============================================================
# IPI for enzyme binding from PMID:21106936
# ============================================================
- term:
    id: GO:0019899
    label: enzyme binding
  evidence_type: IPI
  original_reference_id: PMID:21106936
  review:
    summary: >-
      IPI annotation for enzyme binding from Freeman et al. 2011. The study
      focused on thymosin beta-4 (Tbeta4) as a regulator of cell surface ATP
      synthase in endothelial cells. IF1 was described as having structural
      similarity to Tbeta4 in silico. The WITH column indicates P06576
      (ATP5F1B) and P25705 (ATP5F1A), the beta and alpha subunits of F1-ATP
      synthase.
    action: MODIFY
    reason: >-
      The binding partners (ATP5F1A and ATP5F1B, the alpha and beta subunits
      of F1-ATP synthase) are correct and represent the core binding target
      of IF1. However, "enzyme binding" is too generic. The specific binding
      to the ATP synthase complex is well-characterized and a more specific
      term exists.
    proposed_replacement_terms:
      - id: GO:0140260
        label: mitochondrial proton-transporting ATP synthase complex binding
    supported_by:
      - reference_id: PMID:21106936
        supporting_text: "we identified common amphiphilic alpha-helical structural similarities between beta-thymosins and the inhibitory factor 1 (IF1), an inhibitor of ATP synthase hydrolysis"

# ============================================================
# IMP annotations from PMID:24005319 (continued)
# ============================================================
- term:
    id: GO:1903747
    label: regulation of protein localization to mitochondrion
  evidence_type: IMP
  original_reference_id: PMID:24005319
  review:
    summary: >-
      IMP annotation from Lefebvre et al. 2013. ATPIF1 knockdown prevented
      PARK2 translocation to mitochondria. By promoting mitochondrial
      depolarization (blocking reverse ATP synthase), ATPIF1 enables the
      PINK1-dependent recruitment of PARK2 to damaged mitochondria.
    action: KEEP_AS_NON_CORE
    reason: >-
      This annotation captures a specific aspect of the mitophagy pathway:
      IF1-dependent regulation of PARK2 localization to mitochondria. While
      experimentally supported by the RNAi screen, this is an indirect
      downstream effect. IF1 does not directly regulate protein localization
      machinery; it enables PARK2 recruitment by ensuring mitochondrial
      depolarization through its ATPase inhibitor activity.
    supported_by:
      - reference_id: PMID:24005319
        supporting_text: "we identified ATPase inhibitory factor 1 (ATPIF1/IF1) as essential for PARK2 recruitment and mitophagy in cultured cells"

- term:
    id: GO:0051882
    label: mitochondrial depolarization
  evidence_type: IMP
  original_reference_id: PMID:24005319
  review:
    summary: >-
      IMP annotation from Lefebvre et al. 2013. ATPIF1 promotes collapse
      of the mitochondrial membrane potential during uncoupling by blocking
      the reverse ATPase activity that would otherwise maintain membrane
      potential by pumping protons.
    action: ACCEPT
    reason: >-
      Mitochondrial depolarization is a direct and proximal consequence of
      IF1's core ATPase inhibitor activity. When the electron transport
      chain fails or is uncoupled, ATP synthase reverses to hydrolyze ATP
      and pump protons, partially maintaining membrane potential. IF1 blocks
      this reversal, allowing complete depolarization. This is a direct
      functional outcome and closely tied to the core mechanism. The paper
      states: "During uncoupling, ATPIF1 promotes collapse of delta-psi...
      by blocking the ATPase activity of the F1-Fo ATP synthase."
    supported_by:
      - reference_id: PMID:24005319
        supporting_text: "During uncoupling, ATPIF1 promotes collapse of ΔΨ and activation of the PINK-PARK2 mitophagy pathway by blocking the ATPase activity of the F 1-Fo ATP synthase"
      - reference_id: PMID:24005319
        supporting_text: "Restoration of ATPIF1 in Rho0 cells, which lack mtDNA and a functional electron transport chain, lowers ΔΨ and triggers PARK2 recruitment"

# ============================================================
# HDA annotation for mitochondrion
# ============================================================
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HDA
  original_reference_id: PMID:20833797
  review:
    summary: >-
      HDA annotation for mitochondrial localization from Zhao et al. 2011,
      a phosphoproteomics study of functional mitochondria isolated from
      human muscle. IF1 was detected in the mitochondrial phosphoproteome.
    action: ACCEPT
    reason: >-
      This high-throughput direct assay evidence for mitochondrial
      localization is consistent with all other evidence. The protein
      was identified in isolated mitochondria from human skeletal muscle.
    supported_by:
      - reference_id: PMID:20833797
        supporting_text: "Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphorylation of inner membrane protein complexes and enzymes"

# ============================================================
# ISS for ATPase inhibitor activity
# ============================================================
- term:
    id: GO:0042030
    label: ATPase inhibitor activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for ATPase inhibitor activity transferred from bovine
      ortholog P01096. The bovine IF1 is the best-characterized member of
      this protein family.
    action: ACCEPT
    reason: >-
      This is the core molecular function, and the transfer from the bovine
      ortholog is appropriate given high sequence conservation and identical
      function. Consistent with IDA and IBA annotations for the same term.

# ============================================================
# IDA annotations from PMID:12110673
# ============================================================
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:12110673
  review:
    summary: >-
      IDA annotation for mitochondrial localization from Aggeler et al. 2002.
      IF1 was identified as a subunit of the immunocaptured F1Fo-ATP synthase
      complex from human heart mitochondria and fibroblasts.
    action: ACCEPT
    reason: >-
      Direct experimental evidence from immunocapture of mitochondrial ATP
      synthase complex. IF1 was detected with specific antibody and
      co-purified with the complex from mitochondria.
    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:0042030
    label: ATPase inhibitor activity
  evidence_type: IDA
  original_reference_id: PMID:12110673
  review:
    summary: >-
      IDA annotation for ATPase inhibitor activity from Aggeler et al. 2002.
      The study directly demonstrated that recombinant IF1 inhibited ATP
      hydrolysis by immunocaptured F1Fo-ATP synthase by >90%, and that
      removal of IF1 at pH 8.0 activated the enzyme >10-fold.
    action: ACCEPT
    reason: >-
      This is direct experimental evidence for the core molecular function.
      The quantitative inhibition data (>90% inhibition by recombinant IF1,
      >10-fold activation upon IF1 release) provides strong support for
      ATPase inhibitor activity.
    supported_by:
      - reference_id: PMID:12110673
        supporting_text: "Immunocaptured F(1)F(0) lacking IF(1) could be inhibited by more than 90% by addition of recombinant inhibitor protein, and conversely, F(1)F(0) containing IF(1) could be activated more than 10-fold by brief exposure to pH 8.0, inducing the release of inhibitor protein"

# ============================================================
# Annotations from PMID:15528193 (Burwick et al. 2005)
# ============================================================
- term:
    id: GO:0001525
    label: angiogenesis
  evidence_type: TAS
  original_reference_id: PMID:15528193
  review:
    summary: >-
      TAS annotation for angiogenesis from Burwick et al. 2005. The study
      explored IF1's effect on cell surface ATP synthase in endothelial cells
      and its relationship with angiostatin-mediated anti-angiogenesis. IF1
      was proposed to have a "protective role for EC in the tumor microenvironment"
      that could be overridden by angiostatin.
    action: KEEP_AS_NON_CORE
    reason: >-
      The paper studied IF1 in the context of cell surface ATP synthase and
      angiostatin, concluding that IF1 is NOT an angiostatin mimetic and
      only "slightly inhibited cell proliferation compared with angiostatin."
      The connection to angiogenesis is indirect through the cell surface
      ATP synthase-angiostatin axis. This is a peripheral, non-core function
      related to the unusual cell surface localization of IF1/ATP synthase,
      not the primary mitochondrial function.
    supported_by:
      - reference_id: PMID:15528193
        supporting_text: "We propose that IF1 is not an angiostatin mimetic, but it can serve a protective role for EC in the tumor microenvironment"
      - reference_id: PMID:15528193
        supporting_text: "IF1 did not inhibit EC differentiation to form tubes and only slightly inhibited cell proliferation compared with angiostatin"

- term:
    id: GO:0001937
    label: negative regulation of endothelial cell proliferation
  evidence_type: IDA
  original_reference_id: PMID:15528193
  review:
    summary: >-
      IDA annotation from Burwick et al. 2005 showing that exogenous IF1
      "only slightly inhibited cell proliferation compared with angiostatin."
      The paper explicitly states the effect was minor.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The paper itself states IF1 "only slightly inhibited cell proliferation
      compared with angiostatin." This is a marginal effect observed with
      exogenous IF1 on cell surface ATP synthase, not the protein's primary
      function. The anti-proliferative effect was weak and the authors
      concluded IF1 is "not an angiostatin mimetic." This represents an
      over-annotation of a minor experimental observation.
    supported_by:
      - reference_id: PMID:15528193
        supporting_text: "IF1 did not inhibit EC differentiation to form tubes and only slightly inhibited cell proliferation compared with angiostatin"

- term:
    id: GO:0005516
    label: calmodulin binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for calmodulin binding transferred from bovine ortholog
      P01096. Calmodulin has been reported to interact with IF1 in bovine
      systems, potentially regulating its activity or oligomeric state.
    action: UNDECIDED
    reason: >-
      The calmodulin binding annotation is transferred from the bovine
      ortholog. While there is some evidence for calmodulin-IF1 interaction
      in bovine systems, the physiological significance and whether this
      applies to human IF1 is not well-established in the publications
      available for review. The core regulatory mechanisms of IF1 (pH-dependent
      oligomerization and Ser39 phosphorylation) are well-documented, but
      calmodulin regulation is less certain. Without access to the primary
      bovine literature supporting this claim, this should remain undecided.

- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for mitochondrion transferred from bovine ortholog
      P01096. Consistent with all other evidence for mitochondrial localization.
    action: ACCEPT
    reason: >-
      Mitochondrial localization is well-established for IF1 across species.
      This ISS transfer is consistent with IDA, IBA, IEA, HTP, HDA, and
      TAS evidence for the same localization.

- term:
    id: GO:0009986
    label: cell surface
  evidence_type: IDA
  original_reference_id: PMID:15528193
  review:
    summary: >-
      IDA annotation for cell surface localization from Burwick et al. 2005.
      The study showed IF1 interacting with cell surface F1-ATP synthase on
      endothelial cells. The paper demonstrated IF1 binding to purified F1
      and its effects on cell surface ATP hydrolysis.
    action: KEEP_AS_NON_CORE
    reason: >-
      Cell surface localization of IF1 (and ATP synthase) has been reported
      on endothelial cells. While the primary localization of IF1 is
      mitochondrial, the cell surface localization appears to be a genuine
      but secondary location. The biological significance of cell surface
      IF1 is debated, and it may represent ectopic localization in certain
      cell types rather than a core function.
    supported_by:
      - reference_id: PMID:15528193
        supporting_text: "IF1 protein bound to purified F(1) ATP synthase and inhibited F(1)-dependent ATP hydrolysis consistent with its reported activity in studies of mitochondria"

- term:
    id: GO:0042030
    label: ATPase inhibitor activity
  evidence_type: IDA
  original_reference_id: PMID:15528193
  review:
    summary: >-
      IDA annotation for ATPase inhibitor activity from Burwick et al. 2005.
      The study confirmed IF1 inhibited F1-dependent ATP hydrolysis both
      with purified enzyme and on the cell surface.
    action: ACCEPT
    reason: >-
      The paper directly demonstrates ATPase inhibitor activity, consistent
      with the core function. IF1 inhibited ATP hydrolysis but notably
      "did not inhibit ATP synthesis" on the cell surface, confirming
      its specific ATPase (hydrolysis) inhibitor activity.
    supported_by:
      - reference_id: PMID:15528193
        supporting_text: "IF1 protein bound to purified F(1) ATP synthase and inhibited F(1)-dependent ATP hydrolysis consistent with its reported activity in studies of mitochondria"
      - reference_id: PMID:15528193
        supporting_text: "IF1 inhibited ATP hydrolysis but not ATP synthesis, in contrast to angiostatin, which inhibited both"

- term:
    id: GO:0043532
    label: angiostatin binding
  evidence_type: IDA
  original_reference_id: PMID:15528193
  review:
    summary: >-
      IDA annotation for angiostatin binding from Burwick et al. 2005. The
      study showed that "angiostatin blocks IF1 binding to ATP synthase and
      abolishes its ability to conserve ATP," suggesting overlapping binding
      sites. However, this demonstrates competition for ATP synthase binding,
      not necessarily direct IF1-angiostatin binding.
    action: UNDECIDED
    reason: >-
      The paper demonstrates that angiostatin and IF1 compete for binding
      to ATP synthase, which implies overlapping binding sites on the enzyme
      rather than direct IF1-angiostatin binding. The statement "there is
      a relationship between the binding sites of IF1 and angiostatin on
      ATP synthase" supports competition, not direct binding. Without
      access to the full text to determine whether direct binding was
      actually demonstrated (rather than competition), this remains unclear.
    supported_by:
      - reference_id: PMID:15528193
        supporting_text: "angiostatin blocks IF1 binding to ATP synthase and abolishes its ability to conserve ATP"
      - reference_id: PMID:15528193
        supporting_text: "These data suggest that there is a relationship between the binding sites of IF1 and angiostatin on ATP synthase"

- term:
    id: GO:0051117
    label: ATPase binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for ATPase binding transferred from bovine ortholog
      P01096. Consistent with the IBA and IDA annotations for this term.
    action: ACCEPT
    reason: >-
      ATPase binding is a core function, and this ISS transfer from the
      bovine ortholog is well-supported by multiple experimental evidence
      types for the same term.

- term:
    id: GO:0051117
    label: ATPase binding
  evidence_type: IDA
  original_reference_id: PMID:15528193
  review:
    summary: >-
      IDA annotation for ATPase binding from Burwick et al. 2005. The study
      demonstrated direct binding of IF1 to purified F1 ATP synthase.
    action: ACCEPT
    reason: >-
      The paper directly demonstrates IF1 binding to F1-ATP synthase. This
      is a core function well-supported by multiple lines of evidence.
    supported_by:
      - reference_id: PMID:15528193
        supporting_text: "IF1 protein bound to purified F(1) ATP synthase and inhibited F(1)-dependent ATP hydrolysis"

- term:
    id: GO:0051346
    label: negative regulation of hydrolase activity
  evidence_type: IDA
  original_reference_id: PMID:15528193
  review:
    summary: >-
      IDA annotation for negative regulation of hydrolase activity from
      Burwick et al. 2005. IF1 inhibited ATP hydrolysis activity of the
      F1-ATP synthase both in purified form and on the cell surface.
    action: ACCEPT
    reason: >-
      This annotation accurately captures the core process-level function
      of IF1 at a somewhat general level. IF1 negatively regulates the
      ATP hydrolase activity of F1Fo-ATP synthase. While GO:1905707
      (negative regulation of mitochondrial ATP synthesis coupled proton
      transport) is more specific, this term is also accurate as a broader
      description of the mechanism.
    supported_by:
      - reference_id: PMID:15528193
        supporting_text: "IF1 inhibited ATP hydrolysis but not ATP synthesis"

# ============================================================
# TAS annotations from PMID:10664857 (Ichikawa et al. 1999)
# ============================================================
- term:
    id: GO:0004857
    label: enzyme inhibitor activity
  evidence_type: TAS
  original_reference_id: PMID:10664857
  review:
    summary: >-
      TAS annotation for enzyme inhibitor activity from Ichikawa et al. 1999,
      the paper reporting the human cDNA sequence. The paper describes the
      protein as "the ATPase inhibitor" based on sequence homology to the
      bovine inhibitor protein.
    action: MODIFY
    reason: >-
      While IF1 is indeed an enzyme inhibitor, "enzyme inhibitor activity"
      (GO:0004857) is too general. The more specific term "ATPase inhibitor
      activity" (GO:0042030) is already annotated and better captures the
      specific function. This general term should be replaced with the
      more specific one.
    proposed_replacement_terms:
      - id: GO:0042030
        label: ATPase inhibitor activity
    supported_by:
      - reference_id: PMID:10664857
        supporting_text: "cDNA coding the human homolog of the inhibitor protein was isolated and sequenced"

- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: TAS
  original_reference_id: PMID:10664857
  review:
    summary: >-
      TAS annotation for mitochondrion from Ichikawa et al. 1999. The paper
      describes the protein as "the mitochondrial precursor protein of the
      ATPase inhibitor from humans."
    action: ACCEPT
    reason: >-
      Mitochondrial localization is stated in the paper title and is consistent
      with all other evidence. The paper describes the mitochondrial transit
      peptide and identifies the protein as a mitochondrial ATPase inhibitor.
    supported_by:
      - reference_id: PMID:10664857
        supporting_text: "cDNA coding the mitochondrial precursor protein of the ATPase inhibitor from humans"

- term:
    id: GO:0006091
    label: generation of precursor metabolites and energy
  evidence_type: TAS
  original_reference_id: PMID:10664857
  review:
    summary: >-
      TAS annotation for generation of precursor metabolites and energy from
      Ichikawa et al. 1999. This is a very broad biological process term
      covering all of energy metabolism.
    action: MODIFY
    reason: >-
      This term is too broad. IF1 does not generally participate in
      "generation of precursor metabolites and energy" -- it specifically
      inhibits ATP hydrolysis by the F1Fo-ATP synthase. The more specific
      term GO:1905707 (negative regulation of mitochondrial ATP synthesis
      coupled proton transport) better captures the actual process.
      Alternatively, GO:1903578 (regulation of ATP metabolic process)
      would be more appropriate.
    proposed_replacement_terms:
      - id: GO:1905707
        label: negative regulation of mitochondrial ATP synthesis coupled proton transport

# ============================================================
# NEW annotations suggested based on literature review
# ============================================================
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IDA
  original_reference_id: PMID:12110673
  review:
    summary: >-
      The mature IF1 protein functions in the mitochondrial matrix, where
      it binds the F1 catalytic domain on the matrix-facing side of the
      inner membrane. While "mitochondrion" is annotated, the more specific
      sub-compartment (mitochondrial matrix) is not explicitly annotated.
      UniProt states: "Mitochondrion" as subcellular location, and the
      deep research notes that IF1 acts "on the matrix side of the F1
      catalytic domain." Cryo-EM structures (PDB: 8H9E, 8H9L, 8H9S,
      8H9U, 8KI3) place IF1 bound to the F1 domain which projects into
      the matrix.
    action: NEW
    reason: >-
      The mitochondrial matrix is the specific sub-compartment where
      IF1 is active. The F1 domain that IF1 binds faces the matrix.
      This more specific CC annotation is supported by structural data
      and functional characterization. While "mitochondrion" is annotated,
      the matrix localization should be explicitly noted.
    supported_by:
      - reference_id: PMID:12110673
        supporting_text: "IF(1) could be co-isolated with F(1)F(0) when the immunocapture procedure was carried out at pH 6.5"

core_functions:
- molecular_function:
    id: GO:0042030
    label: ATPase inhibitor activity
  directly_involved_in:
    - id: GO:1905707
      label: negative regulation of mitochondrial ATP synthesis coupled proton transport
    - id: GO:0051882
      label: mitochondrial depolarization
  locations:
    - id: GO:0005759
      label: mitochondrial matrix
  description: >-
    The primary molecular function of ATP5IF1 is ATPase inhibitor activity. IF1
    reversibly inhibits the ATP hydrolase activity of the F1Fo-ATP synthase (complex V)
    by binding the alpha/beta catalytic interface and the gamma subunit of the F1 domain.
    This prevents wasteful ATP consumption when the mitochondrial membrane potential
    collapses during ischemia, hypoxia, or uncoupling. IF1 is active as an antiparallel
    dimer at acidic pH (<6.7) and inactive as a tetramer at neutral pH. Phosphorylation
    at Ser39 by a mitochondrial PKA-like activity inactivates IF1.
  supported_by:
    - reference_id: PMID:12110673
      supporting_text: "Immunocaptured F(1)F(0) lacking IF(1) could be inhibited by more than 90% by addition of recombinant inhibitor protein, and conversely, F(1)F(0) containing IF(1) could be activated more than 10-fold by brief exposure to pH 8.0, inducing the release of inhibitor protein"
    - reference_id: PMID:15528193
      supporting_text: "IF1 protein bound to purified F(1) ATP synthase and inhibited F(1)-dependent ATP hydrolysis consistent with its reported activity in studies of mitochondria"
    - reference_id: file:human/ATP5IF1/ATP5IF1-deep-research-falcon.md
      supporting_text: "IF1 prevents ATP wastage by inhibiting ATP hydrolysis during conditions of low proton motive force (e.g., ischemia/hypoxia), and, depending on cell type and regulation, can also inhibit forward ATP synthesis"
- molecular_function:
    id: GO:0140260
    label: mitochondrial proton-transporting ATP synthase complex binding
  locations:
    - id: GO:0005759
      label: mitochondrial matrix
  description: >-
    IF1 directly binds the F1Fo-ATP synthase complex in a pH-dependent manner.
    At acidic pH (6.5), IF1 co-purifies with the complex; at pH 8.0, IF1 is released.
    The N-terminal inhibitory region (residues 26-52) contacts the alpha/beta subunit
    interface and the gamma subunit. This binding is the mechanistic basis for the
    ATPase inhibitor activity.
  supported_by:
    - reference_id: PMID:12110673
      supporting_text: "IF(1) could be co-isolated with F(1)F(0) when the immunocapture procedure was carried out at pH 6.5 but was absent when the ATP synthase was isolated at pH 8.0"

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: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:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:human/ATP5IF1/ATP5IF1-deep-research-falcon.md
  title: Deep research review of ATP5IF1 gene function (Falcon provider)
  findings:
    - statement: >-
        ATP5IF1 encodes mitochondrial ATPase inhibitory factor 1, a reversible
        pH-sensitive inhibitor of F1Fo-ATP synthase that prevents ATP hydrolysis
        under low proton motive force conditions.
      supporting_text: >-
        IF1 is a reversible, pH-sensitive inhibitor that primarily prevents
        wasteful ATP hydrolysis when Δψm collapses, but can also inhibit ATP
        synthesis in some contexts
- id: PMID:10664857
  title: Nucleotide sequence of cDNA coding the mitochondrial precursor protein of
    the ATPase inhibitor from humans.
  findings:
    - statement: Cloned and sequenced the human IF1 cDNA encoding a 106 amino acid precursor protein
      supporting_text: "The deduced protein sequence shows that the protein was composed of 106 amino acids and had a molecular weight of 12248"
    - statement: Identified the protein as the human homolog of the bovine ATPase inhibitor
      supporting_text: "cDNA coding the human homolog of the inhibitor protein was isolated and sequenced"
- 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: IF1 co-purifies with F1Fo-ATP synthase at pH 6.5 but not at pH 8.0
      supporting_text: "IF(1) could be co-isolated with F(1)F(0) when the immunocapture procedure was carried out at pH 6.5 but was absent when the ATP synthase was isolated at pH 8.0"
    - statement: Recombinant IF1 inhibits ATP hydrolysis by >90%
      supporting_text: "Immunocaptured F(1)F(0) lacking IF(1) could be inhibited by more than 90% by addition of recombinant inhibitor protein"
    - statement: IF1 release at pH 8.0 activates ATP hydrolysis >10-fold
      supporting_text: "F(1)F(0) containing IF(1) could be activated more than 10-fold by brief exposure to pH 8.0, inducing the release of inhibitor protein"
    - statement: IF1 detected by specific antibody in immunocaptured complex from heart mitochondria
      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:15528193
  title: An Inhibitor of the F1 subunit of ATP synthase (IF1) modulates the activity
    of angiostatin on the endothelial cell surface.
  findings:
    - statement: IF1 binds purified F1-ATP synthase and inhibits ATP hydrolysis
      supporting_text: "IF1 protein bound to purified F(1) ATP synthase and inhibited F(1)-dependent ATP hydrolysis consistent with its reported activity in studies of mitochondria"
    - statement: IF1 inhibits ATP hydrolysis but not ATP synthesis on cell surface
      supporting_text: "IF1 inhibited ATP hydrolysis but not ATP synthesis, in contrast to angiostatin, which inhibited both"
    - statement: IF1 only slightly inhibits endothelial cell proliferation
      supporting_text: "IF1 did not inhibit EC differentiation to form tubes and only slightly inhibited cell proliferation compared with angiostatin"
    - statement: IF1 is not an angiostatin mimetic
      supporting_text: "We propose that IF1 is not an angiostatin mimetic, but it can serve a protective role for EC in the tumor microenvironment"
    - statement: Angiostatin blocks IF1 binding to ATP synthase
      supporting_text: "angiostatin blocks IF1 binding to ATP synthase and abolishes its ability to conserve ATP"
- 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:
    - statement: IF1 detected in mitochondrial phosphoproteome from human skeletal muscle
      supporting_text: "We performed a phosphoproteomics study of functional mitochondria isolated from human muscle biopsies"
- id: PMID:21106936
  title: Regenerative protein thymosin beta-4 is a novel regulator of purinergic signaling.
  findings:
    - statement: IF1 shares amphiphilic alpha-helical structural similarities with beta-thymosins
      supporting_text: "in silico we identified common amphiphilic α-helical structural similarities between β-thymosins and the inhibitory factor 1 (IF1), an inhibitor of ATP synthase hydrolysis"
    - statement: IF1 is an inhibitor of ATP synthase hydrolysis
      supporting_text: "the inhibitory factor 1 (IF1), an inhibitor of ATP synthase hydrolysis"
- id: PMID:23135403
  title: Mitochondrial Atpif1 regulates haem synthesis in developing erythroblasts.
  findings:
    - statement: Atpif1 regulates heme synthesis by modulating mitochondrial pH and redox potential
      supporting_text: "Atpif1 modulates the mitochondrial pH and redox potential, and thus allows Fech to efficiently catalyze the incorporation of iron into PPIX to produce heme"
    - statement: Required for FECH to catalyze iron incorporation into protoporphyrin IX
      supporting_text: "Loss of Atpif1 allows the mitochondrial pH and, consequently, the redox potential to change to a level that reduces [2Fe-2S] cluster-containing Fech activity, thereby reducing heme synthesis"
- id: PMID:24005319
  title: Genome-wide RNAi screen identifies ATPase inhibitory factor 1 (ATPIF1) as
    essential for PARK2 recruitment and mitophagy.
  findings:
    - statement: ATPIF1 is essential for PARK2 translocation to mitochondria
      supporting_text: "we identified ATPase inhibitory factor 1 (ATPIF1/IF1) as essential for PARK2 recruitment and mitophagy in cultured cells"
    - statement: ATPIF1 promotes mitochondrial depolarization during uncoupling
      supporting_text: "During uncoupling, ATPIF1 promotes collapse of ΔΨ and activation of the PINK-PARK2 mitophagy pathway by blocking the ATPase activity of the F 1-Fo ATP synthase"
    - statement: ATPIF1 blocks ATPase activity of F1-Fo ATP synthase
      supporting_text: "blocking the ATPase activity of the F 1-Fo ATP synthase"
    - statement: Restoration of ATPIF1 in Rho0 cells lowers membrane potential and triggers PARK2 recruitment
      supporting_text: "Restoration of ATPIF1 in Rho0 cells, which lack mtDNA and a functional electron transport chain, lowers ΔΨ and triggers PARK2 recruitment"
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and disease
    networks.
  findings:
    - statement: ATP5IF1 interacts with ATP5F1B (P06576) in BioPlex 2.0 interactome
- id: PMID:30021884
  title: Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry
    in Intact Cell Nuclei.
  findings:
    - statement: ATP5IF1 crosslinked to ATP5F1B (P06576) detected in nuclear preparations
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings:
    - statement: ATP5IF1 detected interacting with KIF9 and PICK1 in HuRI Y2H screen
- id: PMID:32807793
  title: OSMR controls glioma stem cell respiration and confers resistance of glioblastoma
    to ionizing radiation.
  findings:
    - statement: OSMR detected interacting with ATP5IF1 in mitochondrial context
- id: PMID:32814053
  title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
    and Uncovers Widespread Protein Aggregation in Affected Brains.
  findings:
    - statement: ATP5IF1 detected as interactor of multiple neurodegenerative disease proteins in Y2H screen
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings:
    - statement: ATP5IF1 interacts with ATP5F1B (P06576) in BioPlex 3.0 interactome
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings:
    - statement: ATP5IF1 identified as a high-confidence mitochondrial protein
- id: PMID:35926043
  title: Mitochondrial remodeling and ischemic protection by G protein-coupled receptor
    35 agonists.
  findings:
    - statement: GPR35 binds ATPIF1 at the outer mitochondrial membrane
      supporting_text: "GPR35 activated Gi- and G12/13-coupled signaling and trafficked to the outer mitochondria membrane, where it bound, apparantly indirectly, to ATP synthase inhibitory factor subunit 1 (ATPIF1)"
    - statement: ATPIF1-dependent ATP synthase dimerization prevents ATP loss during ischemia
      supporting_text: "Activated GPR35, in an ATPIF1-dependent and pertussis toxin-sensitive manner, induced ATP synthase dimerization, which prevented ATP loss upon ischemia"
    - statement: Activated GPR35 in pertussis toxin-sensitive manner induces ATP synthase dimerization
      supporting_text: "Activated GPR35, in an ATPIF1-dependent and pertussis toxin-sensitive manner, induced ATP synthase dimerization"
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional genomics.
  findings:
    - statement: ATP5IF1 interacts with ATP5F1B (P06576) in multimodal cell maps