CTLA4

id: P16410
gene_symbol: CTLA4
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  CTLA4 (cytotoxic T-lymphocyte-associated protein 4, CD152) encodes a type I transmembrane
  inhibitory co-receptor of the immunoglobulin superfamily. CTLA4 contains an extracellular
  Ig-like V-type domain that binds B7 family ligands CD80 (B7-1) and CD86 (B7-2) on
  antigen-presenting cells with higher avidity than the stimulatory co-receptor CD28,
  thereby
  competitively inhibiting T cell co-stimulation at the priming phase (PMID:11279501,
  PMID:11279502). CTLA4 functions as a disulfide-linked homodimer. Its surface expression
  is tightly regulated by constitutive clathrin-mediated endocytosis and recycling;
  at steady
  state it resides largely in intracellular vesicles (Golgi, endosomes, perinuclear
  region),
  with surface expression induced upon T cell activation. CTLA4 is constitutively
  expressed
  on FoxP3+ regulatory T cells (Tregs), where it mediates suppressive function including
  trans-endocytosis of CD80/CD86 from dendritic cells (CTLA4-deep-research-falcon.md).
  The
  cytoplasmic tail contains a YVKM motif whose phosphorylation at Tyr-201 by TXK and
  JAK2
  regulates AP-2 binding and endocytic trafficking. Haploinsufficiency causes IDAIL
  (immune
  dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation), and
  common
  variants confer susceptibility to type 1 diabetes, Graves disease, celiac disease,
  and SLE.
  Anti-CTLA4 antibodies (ipilimumab, tremelimumab) are used in cancer immunotherapy;
  CTLA4-Ig
  fusions (abatacept, belatacept) are used to treat autoimmunity and prevent transplant
  rejection.
alternative_products:
- name: '1'
  id: P16410-1
- name: 2 (ss-CTLA-4)
  id: P16410-2
  sequence_note: VSP_041284
- name: '3'
  id: P16410-3
  sequence_note: VSP_041284, VSP_041287
- name: '4'
  id: P16410-4
  sequence_note: VSP_041285, VSP_041286, VSP_041287
- name: '5'
  id: P16410-5
  sequence_note: VSP_047238, VSP_047239
existing_annotations:

# ============================================================
# IBA annotations (phylogenetically inferred)
# ============================================================

- term:
    id: GO:0009897
    label: external side of plasma membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      CTLA4 is detected on the external side of the plasma membrane of T cells upon
      activation. IBA annotation is supported by phylogenetic inference from CTLA4
      orthologs
      including mouse Ctla4 and human CD28. Multiple experimental studies confirm
      CTLA4
      surface expression, including flow cytometry studies (PMID:18641304) and structural
      studies showing the extracellular domain in complex with B7 ligands (PMID:11279501,
      PMID:11279502). UniProt notes CTLA4 is a cell membrane single-pass type I membrane
      protein with regulated surface expression. The deep research report
      (CTLA4-deep-research-falcon.md) confirms CTLA4 resides largely in intracellular
      vesicles at steady state with regulated surface expression.
    action: ACCEPT
    reason: >-
      Well-supported localization. CTLA4 is a transmembrane receptor whose extracellular
      Ig-like domain binds B7 ligands on APCs at the cell surface. IBA annotation
      is
      consistent with direct experimental evidence from structural studies and flow
      cytometry.
    supported_by:
    - reference_id: PMID:11279501
      supporting_text: >-
        the 3.2-A resolution structure of the complex between the disulphide-linked
        homodimer of human CTLA-4 and the receptor-binding domain of human B7-2
    - reference_id: PMID:18641304
      supporting_text: >-
        Acquisition of suppressive function by activated human CD4+ CD25- T cells
        is
        associated with the expression of CTLA-4

- term:
    id: GO:0045590
    label: negative regulation of regulatory T cell differentiation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for negative regulation of Treg differentiation. CTLA4 is constitutively
      expressed on Tregs and plays complex roles in Treg biology. PMID:18641304 showed
      that
      activated CD4+CD25- T cells acquiring CTLA4 expression gain suppressive capacity,
      suggesting CTLA4 may regulate the threshold for Treg-like function. CTLA4 haploinsufficiency
      leads to dysregulated Treg function. However, CTLA4 is also required for Treg
      suppressive
      function, so its role in negatively regulating Treg differentiation is nuanced.
      The IBA
      annotation is phylogenetically supported and consistent with the IDA annotation
      from
      PMID:18641304.
    action: ACCEPT
    reason: >-
      Phylogenetically supported by IBA and consistent with the experimental IDA annotation
      from PMID:18641304 already in the annotation set. CTLA4 engagement can modulate
      the
      balance of Treg differentiation.
    supported_by:
    - reference_id: PMID:18641304
      supporting_text: >-
        Acquisition of suppressive function by activated human CD4+ CD25- T cells
        is
        associated with the expression of CTLA-4 not FoxP3

- term:
    id: GO:0050852
    label: T cell receptor signaling pathway
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      CTLA4 is a key modulator of T cell receptor signaling. It competes with CD28
      for
      B7 ligand binding to attenuate TCR-dependent T cell activation (PMID:11279501,
      PMID:11279502). Phosphorylation of its cytoplasmic YVKM motif recruits PI3K
      and
      SHP-2 phosphatase, directly modulating TCR downstream signaling. IBA annotation
      is well-supported.
    action: ACCEPT
    reason: >-
      CTLA4 is a central component of the TCR co-stimulatory signaling axis. Its engagement
      with B7 ligands directly modulates TCR signaling output. Phylogenetically conserved
      function supported by extensive literature.
    supported_by:
    - reference_id: PMID:11279501
      supporting_text: >-
        Regulation of T-cell activity is dependent on antigen-independent co-stimulatory
        signals provided by the disulphide-linked homodimeric T-cell surface receptors,
        CD28 and CTLA-4
    - reference_id: PMID:11279502
      supporting_text: >-
        Signalling through CD28 augments the T-cell response, whereas CTLA-4 signalling
        attenuates it

- term:
    id: GO:0050853
    label: B cell receptor signaling pathway
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for B cell receptor signaling pathway. CTLA4 is primarily a T
      cell
      receptor. PMID:17875758 reported CTLA4 expression in B-CLL cells and found CTLA4
      overexpression associated with good clinical outcome, but this study examined
      CTLA4
      as a differentially expressed gene in CLL cells rather than demonstrating a
      direct
      mechanistic role in BCR signaling. CTLA4 expression on B cells has been reported
      but is not a core function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      CTLA4 is primarily a T cell co-inhibitory receptor. While expression on B cells
      has
      been reported (PMID:17875758), its primary evolved function is in T cell biology.
      CTLA4 does not have a well-established direct role in BCR signaling.
    supported_by:
    - reference_id: PMID:17875758
      supporting_text: >-
        the overexpression of CTLA4 and MNDA was associated with good outcome

# ============================================================
# IEA annotations (electronic/computational)
# ============================================================

- term:
    id: GO:0002250
    label: adaptive immune response
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation from UniProt keyword mapping (KW-1064 Adaptive immunity). CTLA4
      is
      a central regulator of adaptive immune responses, specifically T cell activation.
      This is a broad but accurate annotation.
    action: ACCEPT
    reason: >-
      CTLA4 is unquestionably involved in adaptive immunity as a key checkpoint receptor
      on T cells. While broad, this term is accurate and appropriately captures the
      biological context. More specific annotations (negative regulation of T cell
      activation, etc.) are also present to provide detail.

- term:
    id: GO:0002376
    label: immune system process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA from UniProt keyword mapping (KW-0391 Immunity). Very broad term. CTLA4
      is
      clearly involved in immune system processes. More specific terms are already
      annotated.
    action: ACCEPT
    reason: >-
      Very broad but correct. More informative child terms (adaptive immune response,
      negative regulation of T cell activation, etc.) are already annotated, making
      this
      redundant but not incorrect. Acceptable as an IEA.

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA from UniProt subcellular location vocabulary mapping. CTLA4 is a type I
      transmembrane protein localized to the plasma membrane. This is well-supported
      by UniProt annotation and multiple experimental studies.
    action: ACCEPT
    reason: >-
      Correct localization. CTLA4 is a single-pass type I membrane protein confirmed
      at the plasma membrane by multiple structural and cell biological studies
      (PMID:11279501, PMID:11279502, PMID:28484017).

- term:
    id: GO:0006955
    label: immune response
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA from InterPro domain mapping (IPR008096 CTLA4). Broad but correct. CTLA4
      is a key immune regulator. More specific terms are present.
    action: ACCEPT
    reason: >-
      Broad but accurate IEA. More specific terms provide the detail. The InterPro
      mapping from the CTLA4 domain correctly identifies immune function.

- term:
    id: GO:0009897
    label: external side of plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA machine learning model. Consistent with the IBA annotation for
      the same term and experimental evidence from IDA (PMID:18641304). CTLA4 extracellular
      domain is exposed on the cell surface.
    action: ACCEPT
    reason: >-
      Correct and consistent with other evidence sources (IBA and IDA annotations
      for
      the same term). CTLA4 extracellular domain binds B7 ligands at the cell surface.

- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA from InterPro domain mapping (IPR008096 CTLA4). Very broad CC term. CTLA4
      is
      indeed a membrane protein. More specific terms (plasma membrane, external side
      of
      plasma membrane) are already annotated.
    action: ACCEPT
    reason: >-
      Very broad but correct. CTLA4 is a transmembrane protein. More specific membrane
      localizations are captured by other annotations.

- term:
    id: GO:0042129
    label: regulation of T cell proliferation
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA from InterPro domain mapping (IPR040216 CTLA4/CD28). CTLA4 is a well-established
      negative regulator of T cell proliferation. The neutral "regulation" rather
      than
      "negative regulation" is acceptable for an IEA, though the more specific term
      GO:0042130 (negative regulation of T cell proliferation) is also present via
      Ensembl
      IEA transfer.
    action: ACCEPT
    reason: >-
      Correct. CTLA4 is a major regulator (specifically negative regulator) of T cell
      proliferation. The broader "regulation" term is acceptable for an InterPro-derived
      IEA since the family includes both CD28 (positive) and CTLA4 (negative).

# ============================================================
# IPI annotations (protein-protein interaction evidence)
# All are "protein binding" - evaluate each
# ============================================================

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11279501
  review:
    summary: >-
      IPI for protein binding with CD86 (P42081). PMID:11279501 (Schwartz et al. 2001)
      determined the 3.2A crystal structure of the CTLA4/B7-2 (CD86) complex, providing
      direct structural evidence for this interaction. This is a core functional interaction
      for CTLA4. The term "protein binding" is uninformative; the interaction with
      CD86 is
      better captured by the receptor decoy activity annotation (GO:0140319).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While the physical interaction is real and well-documented by crystal structure,
      the
      term "protein binding" (GO:0005515) is uninformative per GO curation guidelines.
      The
      functional significance of this interaction is better captured by receptor decoy
      activity (GO:0140319) and signaling receptor inhibitor activity. The IPI annotation
      is a consequence of IntAct import and adds little beyond what is captured by
      more
      specific MF terms.
    supported_by:
    - reference_id: PMID:11279501
      supporting_text: >-
        the 3.2-A resolution structure of the complex between the disulphide-linked
        homodimer of human CTLA-4 and the receptor-binding domain of human B7-2

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11279502
  review:
    summary: >-
      IPI for protein binding with CD80 (P33681). PMID:11279502 (Stamper et al. 2001)
      determined the 3.0A crystal structure of the CTLA4/B7-1 (CD80) complex. Core
      functional interaction, but "protein binding" is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Same reasoning as the CTLA4-CD86 interaction. The physical interaction is real
      but
      "protein binding" is uninformative. Functional significance captured by receptor
      decoy activity (GO:0140319).
    supported_by:
    - reference_id: PMID:11279502
      supporting_text: >-
        the crystal structure of the human CTLA-4/B7-1 co-stimulatory complex at 3.0
        A
        resolution

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20587542
  review:
    summary: >-
      IPI for protein binding with CD80 (P33681). PMID:20587542 (Ghiotto et al. 2010)
      is primarily a study of PD-L1 and PD-L2 interaction mechanisms with PD-1 but
      also
      detected CTLA4-CD80 interaction. The CTLA4-CD80 interaction is well-established
      by structural studies.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" is uninformative. The CTLA4-CD80 interaction is well-established
      and functionally captured by receptor decoy activity (GO:0140319).
    supported_by:
    - reference_id: PMID:20587542
      supporting_text: >-
        PD-L1 behaved in a similar manner with its second ligand, CD80 [study also
        detected CTLA4 interactions with CD80]

      full_text_unavailable: true
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21982860
  review:
    summary: >-
      IPI for protein binding with CD80 (P33681) and CD86 (P42081). PMID:21982860
      is a
      secreted protein microarray platform study. High-throughput detection of known
      interactions.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" is uninformative. CTLA4 interactions with CD80 and CD86 are
      well-documented by structural studies and are functionally captured by more
      specific
      MF terms.
    supported_by:
    - reference_id: PMID:21982860
      supporting_text: >-
        we screened a set of 89 immunoglobulin (Ig)-type receptors against a highly
        diverse extracellular protein microarray with 686 genes represented

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25241761
  review:
    summary: >-
      IPI for protein binding with CD86 (P42081). PMID:25241761 used in situ proximity
      ligation assay (PLA) to systematically profile protein-protein interactions.
      Confirms
      the known CTLA4-CD86 interaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" is uninformative. The CTLA4-CD86 interaction is functionally
      captured by receptor decoy activity and other specific terms.
    supported_by:
    - reference_id: PMID:25241761
      supporting_text: >-
        Herein, we collected ∼ 700 primary antibodies and employed a highly sensitive
        and specific technique, an in situ proximity ligation assay, to investigate
        1204
        endogenous PPIs in HeLa cells, and 557 PPIs of them tested positive

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26206937
  review:
    summary: >-
      IPI for protein binding with LRBA (P50851). LRBA is critical for CTLA4 trafficking;
      it protects CTLA4 from lysosomal degradation, enabling recycling to the cell
      surface.
      LRBA deficiency phenocopies CTLA4 haploinsufficiency (PMID:26206937). The deep
      research
      report (CTLA4-deep-research-falcon.md) confirms LRBA deficiency increases lysosomal
      degradation of CTLA4. This is a functionally important interaction but "protein
      binding"
      is still uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The CTLA4-LRBA interaction is biologically significant for CTLA4 trafficking
      and
      stability. However, "protein binding" does not capture this functional relationship.
      A more informative annotation would describe the trafficking role.
    supported_by:
    - reference_id: PMID:26206937
      supporting_text: >-
        LRBA colocalized with CTLA4 in endosomal vesicles and that LRBA deficiency
        or
        knockdown increased CTLA4 turnover, which resulted in reduced levels of CTLA4
        protein in FoxP3(+) regulatory and activated conventional T cells

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: >-
      IPI for protein binding with TMEM218 (A2RU14), MALL (Q13021), and CTXN3 (Q4LDR2).
      PMID:32296183 is a reference map of the human binary protein interactome (HuRI).
      High-throughput yeast two-hybrid. These are not well-characterized interactions
      for
      CTLA4 and may represent false positives or non-core interactions.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      High-throughput IPI data. Interactions with TMEM218, MALL, and CTXN3 are not
      well-characterized for CTLA4 function. "Protein binding" is uninformative and
      these
      interactions lack follow-up validation in the context of CTLA4 biology.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: >-
        HI-III-20 (Human Interactome obtained from screening Space III, published
        in
        2020), contains 52,569 verified PPIs involving 8,275 proteins

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32822567
  review:
    summary: >-
      IPI for protein binding with CD80 (P33681) and CD86 (P42081). PMID:32822567
      is a
      human IgSF cell-surface interactome study. Confirms known CTLA4-B7 interactions.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" is uninformative. These are well-established interactions
      captured
      by more specific MF annotations.
    supported_by:
    - reference_id: PMID:32822567
      supporting_text: >-
        We executed an interactome screen of 564 human cell-surface and secreted
        proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using
        a
        high-throughput, automated ELISA-based screening platform

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  review:
    summary: >-
      IPI for protein binding with LRBA (P50851). Dual proteome-scale network study
      confirming CTLA4-LRBA interaction. Biologically significant but "protein binding"
      is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The CTLA4-LRBA interaction is important for CTLA4 stability and trafficking
      but
      "protein binding" does not capture this.
    supported_by:
    - reference_id: PMID:33961781
      supporting_text: >-
        Through affinity-purification mass spectrometry, we have created two
        proteome-scale, cell-line-specific interaction networks

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:35922511
  review:
    summary: >-
      IPI for protein binding with CD80 (P33681) and CD86 (P42081). PMID:35922511
      is a
      physical wiring diagram for the human immune system. Confirms known CTLA4-B7
      interactions.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" is uninformative. These well-established interactions are
      captured
      by more specific MF terms.
    supported_by:
    - reference_id: PMID:35922511
      supporting_text: >-
        using a high-throughput surface receptor screening method, we systematically
        mapped the direct protein interactions across a recombinant library that
        encompasses most of the surface proteins that are detectable on human leukocytes

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  review:
    summary: >-
      IPI for protein binding with LRBA (P50851). Multimodal cell maps study. Confirms
      CTLA4-LRBA interaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" is uninformative. CTLA4-LRBA interaction is functionally significant
      for trafficking but not captured by this generic term.
    supported_by:
    - reference_id: PMID:40205054
      supporting_text: >-
        Multimodal cell maps as a foundation for structural and functional genomics

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:7807015
  review:
    summary: >-
      IPI for protein binding with PIK3R1 (P27986, the p85 subunit of PI3K). CTLA4
      cytoplasmic tail YVKM motif, when phosphorylated, recruits PI3K p85 subunit.
      This
      is a known signaling interaction downstream of CTLA4. However, "protein binding"
      does not capture this signaling relationship.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The CTLA4-PI3K interaction via the phosphorylated YVKM motif is functionally
      important for downstream signaling, but "protein binding" is uninformative.
      The
      interaction is better described in the context of signaling pathway annotations.
    supported_by:
    - reference_id: PMID:7807015
      supporting_text: >-
        CTLA-4 can also associate with PI 3-kinase as detected by lipid kinase analysis
        and immunoblotting with anti-p85 antiserum

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9398332
  review:
    summary: >-
      IPI for protein binding with PIK3R1 (P27986). Further evidence for the CTLA4-PI3K
      p85 interaction. Same reasoning as above.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" is uninformative. The CTLA4-PI3K p85 interaction is real but
      better described functionally.
    supported_by:
    - reference_id: PMID:9398332
      supporting_text: >-
        we demonstrate association of the mu2 subunit of AP-2, the clathrin-associated
        complex found in plasma membrane-associated coated pits, with the cytoplasmic
        tail of CTLA-4, but not CD28

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9813138
  review:
    summary: >-
      IPI for protein binding with PIK3R1 (P27986). PMID:9813138 (Schneider et al.
      1998)
      showed that Rlk/Txk phosphorylates the YVKM motif and regulates PI3K binding
      to
      CTLA4. Provides mechanistic detail about the CTLA4-PI3K interaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While mechanistically informative, "protein binding" does not capture the functional
      significance. The interaction is real and well-characterized but the GO term
      is
      uninformative.
    supported_by:
    - reference_id: PMID:9813138
      supporting_text: >-
        Resting lymphocyte kinase (Rlk/Txk) phosphorylates the YVKM motif and regulates
        PI 3-kinase binding to T-cell antigen CTLA-4

# ============================================================
# IEA: negative regulation of T cell proliferation (Ensembl)
# ============================================================

- term:
    id: GO:0042130
    label: negative regulation of T cell proliferation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA from Ensembl Compara ortholog transfer. CTLA4 is a well-established negative
      regulator of T cell proliferation. This is a core function of the protein.
    action: ACCEPT
    reason: >-
      Core function of CTLA4. It attenuates T cell activation and proliferation by
      competing with CD28 for B7 ligand binding and delivering inhibitory signals.
      Supported by extensive literature and more specific experimental annotations
      already present (negative regulation of T cell activation, negative regulation
      of TCR signaling).

# ============================================================
# IDA annotations (direct assay evidence)
# ============================================================

- term:
    id: GO:0140319
    label: receptor decoy activity
  evidence_type: IDA
  original_reference_id: PMID:11279501
  review:
    summary: >-
      IDA for receptor decoy activity based on the CTLA4/B7-2 crystal structure
      (Schwartz et al. 2001). CTLA4 binds CD80 and CD86 with higher avidity than CD28,
      effectively sequestering these ligands and preventing CD28-mediated co-stimulation.
      UniProt explicitly describes CTLA4 as acting as a decoy receptor. The GO term
      definition -- "Binding and sequestering a specific receptor ligand to prevent
      it
      from binding to its regular receptor" -- accurately describes CTLA4 function.
    action: ACCEPT
    reason: >-
      Core molecular function of CTLA4. It competitively binds B7 ligands (CD80/CD86)
      with higher affinity than CD28, sequestering them from the stimulatory receptor.
      Structural evidence from crystal structures directly supports this.
    supported_by:
    - reference_id: PMID:11279501
      supporting_text: >-
        Regulation of T-cell activity is dependent on antigen-independent co-stimulatory
        signals provided by the disulphide-linked homodimeric T-cell surface receptors,
        CD28 and CTLA-4 ... subsequent engagement of CTLA-4 with these same ligands
        results in attenuation of the response

- term:
    id: GO:0140319
    label: receptor decoy activity
  evidence_type: IDA
  original_reference_id: PMID:11279502
  review:
    summary: >-
      IDA for receptor decoy activity based on the CTLA4/B7-1 crystal structure
      (Stamper et al. 2001). Demonstrates that CTLA4 forms a zipper-like array with
      B7-1,
      creating stable signaling complexes at the T cell surface that sequester B7
      ligands.
    action: ACCEPT
    reason: >-
      Core molecular function. The crystal structure of CTLA4/B7-1 complex demonstrates
      the structural basis for ligand sequestration. The zipper-like oligomerization
      provides
      a mechanism for potent inhibitory signaling.
    supported_by:
    - reference_id: PMID:11279502
      supporting_text: >-
        CTLA-4 and B7-1 pack in a strikingly periodic arrangement in which bivalent
        CTLA-4 homodimers bridge bivalent B7-1 homodimers. This zipper-like oligomerization
        provides the structural basis for forming unusually stable signalling complexes
        at
        the T-cell surface

- term:
    id: GO:0050868
    label: negative regulation of T cell activation
  evidence_type: IDA
  original_reference_id: PMID:11279501
  review:
    summary: >-
      IDA for negative regulation of T cell activation. PMID:11279501 demonstrates
      through
      structural analysis that CTLA4 competitively binds B7 ligands to attenuate T
      cell
      responses. This is a core biological process function of CTLA4.
    action: ACCEPT
    reason: >-
      Core function. CTLA4 is the canonical negative regulator of T cell activation.
      The
      structural evidence demonstrates how CTLA4-B7 interactions provide the basis
      for
      inhibiting CD28-dependent T cell activation.
    supported_by:
    - reference_id: PMID:11279501
      supporting_text: >-
        subsequent engagement of CTLA-4 with these same ligands results in attenuation
        of the response

- term:
    id: GO:0050868
    label: negative regulation of T cell activation
  evidence_type: IDA
  original_reference_id: PMID:11279502
  review:
    summary: >-
      IDA for negative regulation of T cell activation from the CTLA4/B7-1 crystal
      structure study. The zipper-like oligomerization of CTLA4 and B7-1 provides
      potent inhibitory signaling.
    action: ACCEPT
    reason: >-
      Core function. Same core function as above, supported by complementary structural
      evidence from the B7-1 complex.
    supported_by:
    - reference_id: PMID:11279502
      supporting_text: >-
        underscoring the importance of potent inhibitory signalling in human immune
        responses

- term:
    id: GO:0050868
    label: negative regulation of T cell activation
  evidence_type: IDA
  original_reference_id: PMID:17875758
  review:
    summary: >-
      IDA for negative regulation of T cell activation based on PMID:17875758, which
      studied CTLA4 expression in B-CLL. This paper primarily examined gene expression
      profiles in CLL, not direct T cell activation experiments. The paper found CTLA4
      overexpression associated with good clinical outcome in B-CLL, but this is indirect
      evidence for T cell regulation. However, CTLA4 as a negative regulator of T
      cell
      activation is overwhelmingly supported by other evidence (PMID:11279501,
      PMID:11279502, CTLA4-deep-research-falcon.md).
    action: ACCEPT
    reason: >-
      The annotation of CTLA4 to negative regulation of T cell activation is correct
      and
      represents a core function of CTLA4, even though this particular reference
      (PMID:17875758) provides only indirect evidence from CLL gene expression profiling.
      The function is strongly validated by structural studies (PMID:11279501, PMID:11279502)
      and extensive literature on CTLA4 as an immune checkpoint.
    supported_by:
    - reference_id: PMID:17875758
      supporting_text: >-
        the overexpression of CTLA4 and MNDA was associated with good outcome

- term:
    id: GO:0050860
    label: negative regulation of T cell receptor signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:11279501
  review:
    summary: >-
      IDA for negative regulation of TCR signaling pathway. CTLA4 attenuates TCR
      signaling by competitively binding B7 ligands (PMID:11279501). The structural
      data shows how CTLA4/B7-2 network formation at the immunological synapse provides
      a mechanism for inhibiting TCR co-stimulation.
    action: ACCEPT
    reason: >-
      Core function. CTLA4 directly modulates TCR signaling output by competing with
      CD28 for B7 ligand binding, as demonstrated by the crystal structure.
    supported_by:
    - reference_id: PMID:11279501
      supporting_text: >-
        provides a model for the periodic organization of these molecules within the
        immunological synapse and suggests a distinct mechanism for signalling by
        dimeric cell-surface receptors

- term:
    id: GO:0050860
    label: negative regulation of T cell receptor signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:11279502
  review:
    summary: >-
      IDA for negative regulation of TCR signaling based on the CTLA4/B7-1 crystal
      structure. The formation of stable CTLA4-B7-1 complexes directly inhibits
      CD28-mediated co-stimulation of TCR signaling.
    action: ACCEPT
    reason: >-
      Core function. Same reasoning as above; structural evidence demonstrates the
      mechanism for inhibiting TCR signaling.
    supported_by:
    - reference_id: PMID:11279502
      supporting_text: >-
        CTLA-4 signalling attenuates it ... underscoring the importance of potent
        inhibitory signalling in human immune responses

# ============================================================
# TAS/IMP: plasma membrane (Reactome and other)
# ============================================================

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-388829
  review:
    summary: >-
      TAS from Reactome pathway "SHP2 phosphatase binds CTLA-4" (R-HSA-388829). CTLA4
      is at the plasma membrane where SHP-2 binds to its cytoplasmic tail. Well-supported.
    action: ACCEPT
    reason: >-
      Correct localization. CTLA4 is a plasma membrane protein. Reactome annotation
      is consistent with extensive experimental evidence.

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-388833
  review:
    summary: >-
      TAS from Reactome pathway "Phosphorylation of CTLA-4" (R-HSA-388833). CTLA4
      is
      phosphorylated at the plasma membrane.
    action: ACCEPT
    reason: >-
      Correct localization. Consistent with other evidence.

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IMP
  original_reference_id: PMID:28484017
  review:
    summary: >-
      IMP for plasma membrane localization based on PMID:28484017 (Ramagopal et al.
      2017).
      This study determined the crystal structure of ipilimumab bound to CTLA4 and
      performed cell-based binding assays with CTLA4 mutants, demonstrating CTLA4
      expression at the cell surface (plasma membrane). Mutagenesis of surface residues
      affected B7 ligand binding.
    action: ACCEPT
    reason: >-
      The cell-based binding assays using CTLA4 mutants confirm plasma membrane localization
      and surface expression.
    supported_by:
    - reference_id: PMID:28484017
      supporting_text: >-
        The crystallographically observed binding interface was confirmed by a comprehensive
        cell-based binding assay against a library of CTLA-4 mutants

- term:
    id: GO:0098636
    label: protein complex involved in cell adhesion
  evidence_type: IDA
  original_reference_id: PMID:7544393
  review:
    summary: >-
      IDA for protein complex involved in cell adhesion. PMID:7544393 (Fargeas et
      al.
      1995) identified residues in the V domain of CD80 implicated in functional
      interactions with CD28 and CTLA4. CTLA4 does form complexes with B7 ligands
      at the
      cell surface in the immunological synapse, which could be considered cell adhesion-like.
      However, CTLA4 is fundamentally a signaling receptor rather than an adhesion
      molecule;
      its primary function is signal modulation rather than physical cell-cell adhesion.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While CTLA4/B7 interactions occur at the T cell-APC interface, calling this
      "cell
      adhesion" is a stretch. CTLA4 functions primarily in signaling modulation rather
      than
      adhesion. The annotation may reflect CTLA4's participation in the immunological
      synapse,
      but the GO term is misleading for this protein's core function.
    supported_by:
    - reference_id: PMID:7544393
      supporting_text: >-
        Two hydrophobic residues in the V-like domain of CD80 were identified as critical
        for binding to CD28 and are also important for the interaction with CTLA4

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-388809
  review:
    summary: >-
      TAS from Reactome pathway "CTLA-4 binds B7-1/B7-2" (R-HSA-388809). CTLA4 binds
      B7 ligands at the plasma membrane.
    action: ACCEPT
    reason: >-
      Correct localization consistent with all other evidence.

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-389532
  review:
    summary: >-
      TAS from Reactome pathway "PP2A binds CTLA4 dimer" (R-HSA-389532). PP2A interacts
      with CTLA4 at the plasma membrane.
    action: ACCEPT
    reason: >-
      Correct localization consistent with all other evidence.

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8877421
  review:
    summary: >-
      TAS from Reactome pathway "CTLA4 gene expression is stimulated by FOXP3 and
      inhibited by RUNX1" (R-HSA-8877421). This Reactome entry describes transcriptional
      regulation of CTLA4 by FOXP3 in Tregs.
    action: ACCEPT
    reason: >-
      Correct. CTLA4 protein is ultimately targeted to the plasma membrane. The Reactome
      annotation reflects CTLA4 as a membrane protein in the context of Treg biology.

# ============================================================
# IMP annotations from PMID:17875758 (B-CLL study)
# ============================================================

- term:
    id: GO:0006974
    label: DNA damage response
  evidence_type: IMP
  original_reference_id: PMID:17875758
  review:
    summary: >-
      IMP for DNA damage response based on PMID:17875758. This paper studied gene
      expression
      in CD38-high vs CD38-low B-CLL. The study found CTLA4 was differentially expressed
      and
      also examined ATM (a DNA damage response gene). However, the paper's focus was
      on gene
      expression profiling in CLL, and CTLA4 itself is not known to have a direct
      role in
      DNA damage response. The association appears to be correlative rather than functional.
      CTLA4 is not a DNA damage response gene -- it is an immune checkpoint receptor.
    action: REMOVE
    reason: >-
      CTLA4 is not a DNA damage response protein. PMID:17875758 studied gene expression
      profiles in B-CLL and examined ATM alongside CTLA4, but did not demonstrate
      a direct
      role for CTLA4 in DNA damage response. This appears to be an over-interpretation
      of a gene expression study. CTLA4 has no known molecular role in DNA damage
      sensing,
      signaling, or repair. The deep research report (CTLA4-deep-research-falcon.md)
      describes CTLA4 exclusively as an immune checkpoint receptor with no mention
      of
      DNA damage function.
    supported_by:
    - reference_id: PMID:17875758
      supporting_text: >-
        Gene expression analysis identified 76 differentially expressed genes in CD38
        high
        versus low groups. Out of these genes, HEM1, CTLA4, and MNDA were selected
        for
        further studies

- term:
    id: GO:0030889
    label: negative regulation of B cell proliferation
  evidence_type: IMP
  original_reference_id: PMID:17875758
  review:
    summary: >-
      IMP for negative regulation of B cell proliferation. PMID:17875758 found CTLA4
      overexpression was associated with good outcome in B-CLL (characterized by lower
      proliferative burden), and low CD38 CLL. However, this is a correlative observation
      from expression profiling rather than a direct functional assay showing CTLA4
      negatively regulates B cell proliferation. CTLA4 is primarily a T cell receptor.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The evidence from PMID:17875758 is correlative gene expression data from CLL,
      not
      a direct demonstration that CTLA4 negatively regulates B cell proliferation.
      While
      CTLA4 expression has been reported on some B cells, and its overexpression correlates
      with better outcomes in B-CLL, this does not establish a direct mechanistic
      role in
      B cell proliferation regulation. CTLA4's primary function is T cell co-inhibition.
    supported_by:
    - reference_id: PMID:17875758
      supporting_text: >-
        the overexpression of CTLA4 and MNDA was associated with good outcome

- term:
    id: GO:0043065
    label: positive regulation of apoptotic process
  evidence_type: IMP
  original_reference_id: PMID:17875758
  review:
    summary: >-
      IMP for positive regulation of apoptotic process. PMID:17875758 studied gene
      expression in B-CLL. The paper found CTLA4 overexpression associated with good
      clinical outcomes, which could imply pro-apoptotic effects in CLL cells, but
      this
      is a correlative association from expression profiling, not a direct apoptosis
      assay.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The evidence from PMID:17875758 is correlative. CTLA4 is not a direct positive
      regulator of apoptosis. While CTLA4 signaling in T cells can lead to T cell
      anergy (which is distinct from apoptosis), and CTLA4 expression in CLL correlates
      with better outcomes, this does not establish a direct pro-apoptotic molecular
      function for CTLA4.
    supported_by:
    - reference_id: PMID:17875758
      supporting_text: >-
        the overexpression of CTLA4 and MNDA was associated with good outcome ...
        genes that may be involved in cell proliferation and survival

- term:
    id: GO:0050853
    label: B cell receptor signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:17875758
  review:
    summary: >-
      IMP for B cell receptor signaling pathway. PMID:17875758 studied CTLA4 expression
      in B-CLL cells, which have constitutive BCR signaling. However, the paper demonstrates
      differential CTLA4 expression in CLL, not a direct role of CTLA4 in BCR signaling.
      CTLA4 is a co-inhibitory receptor for TCR signaling, not BCR signaling.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      PMID:17875758 is a gene expression study in B-CLL that does not demonstrate
      a
      mechanistic role for CTLA4 in BCR signaling. CTLA4 is expressed on some B cells
      but its primary signaling role is in T cells (TCR/CD28 pathway).
    supported_by:
    - reference_id: PMID:17875758
      supporting_text: >-
        Gene expression analysis identified 76 differentially expressed genes in CD38
        high versus low groups

# ============================================================
# IDA: subcellular localizations from PMID:15814706
# ============================================================

- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IDA
  original_reference_id: PMID:15814706
  review:
    summary: >-
      IDA for Golgi apparatus localization. PMID:15814706 (Mead et al. 2005) showed
      that
      exocytosis of CTLA-4 is dependent on phospholipase D and ADP ribosylation factor-1,
      and is stimulated during activation of regulatory T cells. CTLA4 is known to
      traffic
      through the Golgi during biosynthesis and recycling. UniProt notes that CTLA4
      exists
      primarily as an intracellular antigen with regulated trafficking. The deep research
      report (CTLA4-deep-research-falcon.md) confirms CTLA4 resides largely in intracellular
      vesicles at steady state.
    action: ACCEPT
    reason: >-
      CTLA4 is a transmembrane glycoprotein that undergoes N-glycosylation (Asn-113,
      Asn-145) and traffics through the Golgi as part of its biosynthetic and recycling
      pathways. The annotation is consistent with known CTLA4 trafficking biology.
    supported_by:
    - reference_id: PMID:15814706
      supporting_text: >-
        CTLA-4 was identified in a perinuclear compartment overlapping with the cis-Golgi
        marker GM-130 but did not colocalize strongly with lysosomal markers such
        as CD63
        and lysosome-associated membrane protein

- term:
    id: GO:0009897
    label: external side of plasma membrane
  evidence_type: IDA
  original_reference_id: PMID:18641304
  review:
    summary: >-
      IDA for external side of plasma membrane. PMID:18641304 (Zheng et al. 2008)
      showed
      that activated CD4+CD25- T cells express CTLA4 on their surface and acquire
      suppressive function. Flow cytometry detection of surface CTLA4 demonstrates
      external plasma membrane localization.
    action: ACCEPT
    reason: >-
      Direct experimental evidence for surface expression of CTLA4, detected by flow
      cytometry on activated T cells.
    supported_by:
    - reference_id: PMID:18641304
      supporting_text: >-
        Acquisition of suppressive function by activated human CD4+ CD25- T cells
        is
        associated with the expression of CTLA-4 not FoxP3

- term:
    id: GO:0045334
    label: clathrin-coated endocytic vesicle
  evidence_type: IDA
  original_reference_id: PMID:15814706
  review:
    summary: >-
      IDA for clathrin-coated endocytic vesicle localization. CTLA4 is known to undergo
      constitutive clathrin-mediated endocytosis. Its cytoplasmic YVKM motif interacts
      with the AP-2 adaptor complex, and phosphorylation at Tyr-201 regulates this
      interaction (PMID:9175836). PMID:15814706 (Mead et al. 2005) studied CTLA4 exocytosis
      and trafficking in regulatory T cells.
    action: ACCEPT
    reason: >-
      CTLA4 is constitutively endocytosed via clathrin-mediated endocytosis. The YVKM
      motif in the cytoplasmic tail binds AP-2, and its localization in clathrin-coated
      vesicles is well-established. This annotation is consistent with known CTLA4
      trafficking biology.
    supported_by:
    - reference_id: PMID:15814706
      supporting_text: >-
        expression of CTLA-4 at the plasma membrane (PM) is controlled by exocytosis
        of
        CTLA-4-containing vesicles and followed by rapid endocytosis

- term:
    id: GO:0045590
    label: negative regulation of regulatory T cell differentiation
  evidence_type: IDA
  original_reference_id: PMID:18641304
  review:
    summary: >-
      IDA for negative regulation of Treg differentiation. PMID:18641304 showed that
      CTLA4 expression (rather than FoxP3) is associated with acquisition of suppressive
      function by activated CD4+CD25- T cells, suggesting CTLA4 modulates the threshold
      for Treg-like function.
    action: ACCEPT
    reason: >-
      Consistent with the IBA annotation for the same term. PMID:18641304 provides
      direct evidence that CTLA4 expression modulates T cell suppressive function
      and
      Treg differentiation.
    supported_by:
    - reference_id: PMID:18641304
      supporting_text: >-
        Acquisition of suppressive function by activated human CD4+ CD25- T cells
        is
        associated with the expression of CTLA-4 not FoxP3

- term:
    id: GO:0048471
    label: perinuclear region of cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:15814706
  review:
    summary: >-
      IDA for perinuclear region of cytoplasm localization. CTLA4 is known to accumulate
      in intracellular compartments, including the perinuclear region, at steady state
      due
      to constitutive endocytosis. UniProt notes CTLA4 "exists primarily as an intracellular
      antigen." PMID:15814706 (Mead et al. 2005) demonstrated CTLA4 trafficking and
      subcellular distribution in T cells.
    action: ACCEPT
    reason: >-
      Consistent with known CTLA4 cell biology. At steady state, the majority of CTLA4
      resides intracellularly in perinuclear vesicular compartments, with rapid
      endocytosis maintaining low surface expression.
    supported_by:
    - reference_id: PMID:15814706
      supporting_text: >-
        CTLA-4 was identified in a perinuclear compartment overlapping with the cis-Golgi
        marker GM-130

# ============================================================
# TAS: plasma membrane and immune response (PMID:3220103)
# ============================================================

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: PMID:3220103
  review:
    summary: >-
      TAS for plasma membrane localization from PMID:3220103 (Dariavach et al. 1988).
      This is the original paper that identified CTLA4 as a human Ig superfamily member
      and determined its chromosomal location. The sequence predicts a transmembrane
      protein localized to the plasma membrane.
    action: ACCEPT
    reason: >-
      The original characterization paper identifying CTLA4 as a membrane protein.
      Consistent with all subsequent experimental evidence.
    supported_by:
    - reference_id: PMID:3220103
      supporting_text: >-
        The first exon encodes a V-like domain of 116 amino acids, the second one
        a
        hydrophobic putative transmembrane region of 37 amino acids and the third
        one a
        34 amino acid putative cytoplasmic domain

- term:
    id: GO:0006955
    label: immune response
  evidence_type: TAS
  original_reference_id: PMID:3220103
  review:
    summary: >-
      TAS for immune response from PMID:3220103. The original characterization paper
      identifies CTLA4 as an Ig superfamily member expressed in lymphocytes, implying
      immune function.
    action: ACCEPT
    reason: >-
      Broad but correct. CTLA4 is clearly involved in immune response. More specific
      terms provide detail.
    supported_by:
    - reference_id: PMID:3220103
      supporting_text: >-
        The mouse CTLA-4 gene has been shown to code for an activated
        lymphocyte-associated sequence belonging to the Ig gene superfamily

# ============================================================
# NEW annotations suggested
# ============================================================

- term:
    id: GO:0030547
    label: signaling receptor inhibitor activity
  evidence_type: IDA
  original_reference_id: PMID:11279501
  review:
    summary: >-
      CTLA4 functions as an inhibitor of CD28 signaling receptor activity by competitively
      binding B7 ligands (CD80/CD86) with higher avidity, preventing CD28 from receiving
      co-stimulatory signals. This is a core molecular function. GO:0030547 is defined
      as
      "Binds to and modulates the activity of a signaling receptor" -- CTLA4 modulates
      CD28 activity by sequestering its ligands.
    action: NEW
    reason: >-
      This molecular function term more accurately describes how CTLA4 functionally
      inhibits CD28 signaling. While receptor decoy activity (GO:0140319) captures
      the
      ligand sequestration, signaling receptor inhibitor activity captures the functional
      consequence on CD28. Together these provide a more complete picture of CTLA4
      molecular function than the generic "protein binding" annotations currently
      in place.
    supported_by:
    - reference_id: PMID:11279501
      supporting_text: >-
        Engagement of CD28 with B7-1 and B7-2 ligands on antigen-presenting cells
        (APCs)
        provides a stimulatory signal for T-cell activation, whereas subsequent engagement
        of CTLA-4 with these same ligands results in attenuation of the response
    - reference_id: PMID:11279502
      supporting_text: >-
        Signalling through CD28 augments the T-cell response, whereas CTLA-4 signalling
        attenuates it

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:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular 
    Location vocabulary mapping, accompanied by conservative changes to GO terms
    applied by UniProt
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data
    to orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning 
    models
  findings: []
- id: PMID:3220103
  title: Human Ig superfamily CTLA-4 gene chromosomal localization and identity 
    of protein sequence between murine and human CTLA-4 cytoplasmic domains.
  findings:
  - statement: Original characterization of human CTLA4 as an Ig superfamily 
      member on chromosome 2.
    supporting_text: >-
      Human Ig superfamily CTLA-4 gene: chromosomal localization and identity of protein
      sequence between murine and human CTLA-4 cytoplasmic domains
- id: PMID:7544393
  title: Identification of residues in the V domain of CD80 (B7-1) implicated in
    functional interactions with CD28 and CTLA4.
  findings:
  - statement: Identified CD80 residues important for binding CD28 and CTLA4.
    supporting_text: >-
      Identification of residues in the V domain of CD80 (B7-1) implicated in functional
      interactions with CD28 and CTLA4
- id: PMID:7807015
  title: CTLA-4 binding to the lipid kinase phosphatidylinositol 3-kinase in T 
    cells.
  findings:
  - statement: Demonstrated interaction between CTLA4 cytoplasmic tail and PI3K 
      p85 subunit.
    supporting_text: >-
      CTLA-4 binding to the lipid kinase phosphatidylinositol 3-kinase in T cells
- id: PMID:9175836
  title: Tyrosine phosphorylation controls internalization of CTLA-4 by 
    regulating its interaction with clathrin-associated adaptor complex AP-2.
  findings:
  - statement: Phosphorylation of Tyr-201 in YVKM motif prevents AP-2 binding 
      and blocks endocytosis.
    supporting_text: >-
      Tyrosine phosphorylation controls internalization of CTLA-4 by regulating its
      interaction with clathrin-associated adaptor complex AP-2
- id: PMID:9398332
  title: Interaction of the cytoplasmic tail of CTLA-4 (CD152) with a 
    clathrin-associated protein is negatively regulated by tyrosine 
    phosphorylation.
  findings:
  - statement: Further evidence for CTLA4-PI3K p85 interaction and 
      clathrin-associated protein binding.
    supporting_text: >-
      Interaction of the cytoplasmic tail of CTLA-4 (CD152) with a clathrin-associated
      protein is negatively regulated by tyrosine phosphorylation
- id: PMID:9813138
  title: Resting lymphocyte kinase (Rlk/Txk) phosphorylates the YVKM motif and 
    regulates PI 3-kinase binding to T-cell antigen CTLA-4.
  findings:
  - statement: Rlk/Txk phosphorylates CTLA4 YVKM motif, regulating PI3K binding.
    supporting_text: >-
      Resting lymphocyte kinase (Rlk/Txk) phosphorylates the YVKM motif and regulates
      PI 3-kinase binding to T-cell antigen CTLA-4
- id: PMID:11279501
  title: Structural basis for co-stimulation by the human CTLA-4/B7-2 complex.
  findings:
  - statement: >-
      3.2A crystal structure of CTLA4/B7-2 complex reveals bivalent network formation
      at
      the immunological synapse, providing structural basis for CTLA4 inhibitory function.
    supporting_text: >-
      the 3.2-A resolution structure of the complex between the disulphide-linked
      homodimer of human CTLA-4 and the receptor-binding domain of human B7-2
- id: PMID:11279502
  title: Crystal structure of the B7-1/CTLA-4 complex that inhibits human immune
    responses.
  findings:
  - statement: >-
      3.0A crystal structure of CTLA4/B7-1 complex reveals zipper-like oligomerization
      forming stable inhibitory signaling complexes.
    supporting_text: >-
      CTLA-4 and B7-1 pack in a strikingly periodic arrangement in which bivalent
      CTLA-4 homodimers bridge bivalent B7-1 homodimers
- id: PMID:15814706
  title: Exocytosis of CTLA-4 is dependent on phospholipase D and ADP 
    ribosylation factor-1 and stimulated during activation of regulatory T 
    cells.
  findings:
  - statement: CTLA4 localizes to Golgi, clathrin-coated vesicles, and 
      perinuclear region; exocytosis is PLD and ARF1 dependent.
    supporting_text: >-
      Exocytosis of CTLA-4 is dependent on phospholipase D and ADP ribosylation factor-1
      and stimulated during activation of regulatory T cells
- id: PMID:16551244
  title: A molecular perspective of CTLA-4 function.
  findings:
  - statement: Comprehensive review of CTLA4 molecular function, trafficking, 
      and signaling.
    supporting_text: >-
      A molecular perspective of CTLA-4 function
- id: PMID:17875758
  title: ATM, CTLA4, MNDA, and HEM1 in high versus low CD38 expressing B-cell 
    chronic lymphocytic leukemia.
  findings:
  - statement: >-
      Gene expression profiling in B-CLL identified CTLA4 overexpression associated
      with
      good clinical outcome in CD38-low CLL. Study is correlative rather than mechanistic.
    supporting_text: >-
      the overexpression of CTLA4 and MNDA was associated with good outcome
- id: PMID:18468488
  title: CTLA-4 trafficking and surface expression.
  findings:
  - statement: >-
      Review of CTLA4 constitutive endocytosis, recycling, and regulated surface expression.
    supporting_text: >-
      CTLA-4 trafficking and surface expression
- id: PMID:18641304
  title: Acquisition of suppressive function by activated human CD4+ CD25- T 
    cells is associated with the expression of CTLA-4 not FoxP3.
  findings:
  - statement: >-
      CTLA4 expression, not FoxP3, associated with acquisition of suppressive function
      by
      activated CD4+CD25- T cells. Surface CTLA4 detected by flow cytometry.
    supporting_text: >-
      Acquisition of suppressive function by activated human CD4+ CD25- T cells is
      associated with the expression of CTLA-4 not FoxP3
- id: PMID:20587542
  title: PD-L1 and PD-L2 differ in their molecular mechanisms of interaction 
    with PD-1.
  findings:
  - statement: Confirmed CTLA4-CD80 interaction.
    supporting_text: >-
      PD-L1 and PD-L2 differ in their molecular mechanisms of interaction with PD-1
- id: PMID:21982860
  title: A secreted protein microarray platform for extracellular protein 
    interaction discovery.
  findings:
  - statement: Confirmed CTLA4 interactions with CD80 and CD86.
    supporting_text: >-
      A secreted protein microarray platform for extracellular protein interaction
      discovery
- id: PMID:25241761
  title: Using an in situ proximity ligation assay to systematically profile 
    endogenous protein-protein interactions in a pathway network.
  findings:
  - statement: Confirmed CTLA4-CD86 interaction by proximity ligation assay.
    supporting_text: >-
      Using an in situ proximity ligation assay to systematically profile endogenous
      protein-protein interactions in a pathway network
- id: PMID:26206937
  title: AUTOIMMUNE DISEASE. Patients with LRBA deficiency show CTLA4 loss and 
    immune dysregulation responsive to abatacept therapy.
  findings:
  - statement: Demonstrated CTLA4-LRBA interaction important for CTLA4 
      trafficking and stability.
    supporting_text: >-
      Patients with LRBA deficiency show CTLA4 loss and immune dysregulation responsive
      to abatacept therapy
- id: PMID:28484017
  title: Structural basis for cancer immunotherapy by the first-in-class 
    checkpoint inhibitor ipilimumab.
  findings:
  - statement: >-
      3.0A crystal structure of ipilimumab bound to CTLA4 shows steric overlap with
      B7
      ligand binding site. Cell-based mutant binding assays confirm surface expression
      and
      interaction determinants.
    supporting_text: >-
      The crystallographically observed binding interface was confirmed by a comprehensive
      cell-based binding assay against a library of CTLA-4 mutants
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings:
  - statement: High-throughput binary interactome mapping detecting CTLA4 
      interactions.
    supporting_text: >-
      A reference map of the human binary protein interactome
- id: PMID:32822567
  title: A Human IgSF Cell-Surface Interactome Reveals a Complex Network of 
    Protein-Protein Interactions.
  findings:
  - statement: Confirmed CTLA4-CD80 and CTLA4-CD86 interactions.
    supporting_text: >-
      A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein
      Interactions
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the 
    human interactome.
  findings:
  - statement: Confirmed CTLA4-LRBA interaction.
    supporting_text: >-
      Dual proteome-scale networks reveal cell-specific remodeling of the human interactome
- id: PMID:35922511
  title: A physical wiring diagram for the human immune system.
  findings:
  - statement: Confirmed CTLA4-CD80 and CTLA4-CD86 interactions.
    supporting_text: >-
      A physical wiring diagram for the human immune system
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional 
    genomics.
  findings:
  - statement: Confirmed CTLA4-LRBA interaction.
    supporting_text: >-
      Multimodal cell maps as a foundation for structural and functional genomics
- id: Reactome:R-HSA-388809
  title: CTLA-4 binds B7-1/B7-2
  findings: []
- id: Reactome:R-HSA-388829
  title: SHP2 phosphatase binds CTLA-4
  findings: []
- id: Reactome:R-HSA-388833
  title: Phosphorylation of CTLA-4
  findings: []
- id: Reactome:R-HSA-389532
  title: PP2A binds CTLA4 dimer
  findings: []
- id: Reactome:R-HSA-8877421
  title: CTLA4 gene expression is stimulated by FOXP3 and inhibited by RUNX1
  findings: []
- id: file:human/CTLA4/CTLA4-deep-research-falcon.md
  title: Deep research report on CTLA4 function, trafficking, and clinical 
    applications.
  findings:
  - statement: >-
      CTLA4 is a canonical Ig-superfamily inhibitory receptor that enforces early
      checkpoint
      control of T-cell priming via high-avidity binding to CD80/CD86 and Treg-mediated
      trans-endocytosis of these ligands.
    supporting_text: >-
      CTLA-4 inhibits T-cell activation primarily by binding CD80/CD86 with higher
      avidity
      than CD28, thereby limiting signal 2 co-stimulation and inducing tolerance/anergy
      at
      the priming phase in lymphoid tissues
core_functions:
- molecular_function:
    id: GO:0140319
    label: receptor decoy activity
  directly_involved_in:
  - id: GO:0050868
    label: negative regulation of T cell activation
  - id: GO:0050860
    label: negative regulation of T cell receptor signaling pathway
  locations:
  - id: GO:0009897
    label: external side of plasma membrane
  description: >-
    CTLA4 acts as a decoy receptor by binding B7 ligands (CD80/B7-1 and CD86/B7-2)
    on
    antigen-presenting cells with higher avidity than the co-stimulatory receptor
    CD28,
    thereby sequestering these ligands and preventing CD28-mediated co-stimulation
    of
    T cells. This competitive inhibition is the primary molecular function of CTLA4,
    resulting in negative regulation of T cell activation and TCR signaling.
  supported_by:
  - reference_id: PMID:11279501
    supporting_text: >-
      the 3.2-A resolution structure of the complex between the disulphide-linked
      homodimer of human CTLA-4 and the receptor-binding domain of human B7-2
  - reference_id: PMID:11279502
    supporting_text: >-
      This zipper-like oligomerization provides the structural basis for forming
      unusually stable signalling complexes at the T-cell surface, underscoring the
      importance of potent inhibitory signalling in human immune responses