ORMDL3

id: Q8N138
gene_symbol: ORMDL3
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  ORMDL3 (ORM1-like protein 3) is a conserved, multi-pass transmembrane protein
  of 153 amino acids that resides in the endoplasmic reticulum (ER) membrane. It
  functions as a ceramide-sensitive regulatory subunit of the serine
  palmitoyltransferase (SPT) complex (SPTLC1/SPTLC2/ssSPTa/ORMDL3), the enzyme
  that catalyzes the first and rate-limiting step in de novo sphingolipid
  biosynthesis. ORMDL3 acts as a negative regulator of SPT: its N-terminus
  physically occludes the substrate entry tunnel of SPT, and this inhibitory
  conformation is stabilized by ceramide binding, thereby implementing a
  homeostatic negative feedback loop that maintains sphingolipid levels.
  Structurally resolved by cryo-EM, ORMDL3 has four transmembrane helices and a
  cytoplasmic N-terminal ceramide-sensing region. The 17q21 locus containing
  ORMDL3 is the strongest and most replicated genetic risk locus for childhood
  asthma. Beyond sphingolipid regulation, ORMDL3 has been implicated in ER
  stress/UPR signaling, ER calcium homeostasis, and autophagy regulation in
  immune cells, though these may represent downstream consequences of altered
  sphingolipid metabolism rather than independent molecular functions.
alternative_products:
- name: '1'
  id: Q8N138-1
- name: '2'
  id: Q8N138-4
  sequence_note: VSP_016052
existing_annotations:
# --- IBA annotations (phylogenetic inference) ---
- term:
    id: GO:0030148
    label: sphingolipid biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      ORMDL3 is a regulatory subunit of the SPT complex that controls the
      rate-limiting step in sphingolipid de novo biosynthesis. The IBA annotation
      to sphingolipid biosynthetic process is well supported by the conserved
      role of ORM/ORMDL family proteins in sphingolipid metabolism from yeast to
      human (PMID:20182505, PMID:33558761).
    action: ACCEPT
    reason: >-
      Core function. ORMDL3 is an integral component of the SPT complex and
      directly regulates sphingolipid biosynthetic flux. This is phylogenetically
      conserved across the ORM family.
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        Orm family proteins mediate sphingolipid homeostasis... we identify Orm
        proteins as negative regulators of sphingolipid synthesis that form a
        conserved complex with serine palmitoyltransferase, the first and
        rate-limiting enzyme in sphingolipid production.
    - reference_id: PMID:33558761
      supporting_text: >-
        the first and rate-limiting step of sphingolipid synthesis is catalyzed
        by the serine palmitoyltransferase holocomplex, which consists of
        catalytic components (SPTLC1 and SPTLC2) and regulatory components
        (ssSPTa and ORMDL3).
    additional_reference_ids:
    - file:human/ORMDL3/ORMDL3-deep-research-falcon.md

- term:
    id: GO:0090156
    label: intracellular sphingolipid homeostasis
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      ORMDL3 implements ceramide-dependent negative feedback on SPT to maintain
      sphingolipid homeostasis. Ceramide binding to the ORMDL3 N-terminus
      stabilizes an inhibitory conformation that blocks SPT substrate entry,
      constituting a homeostatic sensor mechanism (PMID:20182505,
      PMID:37308477).
    action: ACCEPT
    reason: >-
      Core function. ORMDL3 is the ceramide-sensing subunit of the SPT complex
      that provides homeostatic feedback regulation of sphingolipid levels. This
      is the primary evolved role of the ORM/ORMDL family.
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        Orm proteins are dynamic negative regulators of serine
        palmitoyltransferase whose inhibitory activity is dependent on adequate
        levels of downstream sphingolipids
    - reference_id: PMID:37308477
      supporting_text: >-
        Structural studies indicate that ceramide can induce and lock the
        N-terminus of ORMDL3 into an inhibitory conformation.

- term:
    id: GO:0017059
    label: serine palmitoyltransferase complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      ORMDL3 is a stoichiometric subunit of the SPT complex. The phylogenetic
      inference is consistent with conserved physical association of ORM/ORMDL
      proteins with SPT from yeast to human, confirmed by co-IP and cryo-EM
      structural studies (PMID:20182505, PMID:33558761, PMID:33558762).
    action: ACCEPT
    reason: >-
      Core localization. Structural and biochemical data confirm ORMDL3 is an
      integral subunit of the SPT holoenzyme complex.
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        Immunoprecipitations from HEK293T cells expressing 3×Flag-tagged Ormdl3
        led to a prominent Sptlc1 band detected by Western blot (Fig

- term:
    id: GO:0006672
    label: ceramide metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      ORMDL3 regulates ceramide levels by controlling SPT activity, the
      rate-limiting step upstream of ceramide synthesis. This IBA annotation is
      phylogenetically sound, as yeast ORM proteins also regulate ceramide
      levels (PMID:20182505).
    action: ACCEPT
    reason: >-
      Ceramide levels are directly controlled by ORMDL3-mediated regulation of
      SPT. Loss of ORM/ORMDL function leads to elevated ceramide levels in both
      yeast and human cells.
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        we found that simultaneous knock-down by RNAi of ORMDL1/2/3 in Hela
        cells causes an approximately three-fold increase in ceramide levels

# --- IEA annotations (electronic inference) ---
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      ORMDL3 is an ER membrane-resident multi-pass transmembrane protein. This
      IEA is consistent with experimental data showing ER membrane localization
      by GFP-tagging (PMID:12093374), immunofluorescence (PMID:19819884), and
      cryo-EM structures showing ORMDL3 embedded in the membrane within the SPT
      complex (PMID:33558761, PMID:33558762).
    action: ACCEPT
    reason: >-
      Correct and well-supported. UniProt annotation from subcellular
      localization data; multiple experimental lines confirm ER membrane
      localization.
    supported_by:
    - reference_id: PMID:12093374
      supporting_text: >-
        fusion proteins of enhanced green fluorescent protein and ORMDL
        (EGFP-ORMDL) appeared predominantly in the perinuclear endoplasmic
        reticulum (ER) and, to a lesser extent, throughout the extended ER
        network

- term:
    id: GO:0006665
    label: sphingolipid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation to sphingolipid metabolic process from ARBA. This is
      correct but broader than the more specific IBA annotations already present
      (GO:0030148 sphingolipid biosynthetic process, GO:0090156 intracellular
      sphingolipid homeostasis).
    action: ACCEPT
    reason: >-
      Correct parent term. Although more specific terms are already annotated
      via IBA, this broader IEA annotation is not wrong and reflects the general
      role of ORMDL3 in sphingolipid metabolism.

- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Generic membrane annotation from InterPro domain mapping. ORMDL3 is
      indeed a multi-pass transmembrane protein with four transmembrane helices.
    action: ACCEPT
    reason: >-
      Correct but very generic. More specific ER membrane annotation is also
      present. This is an acceptable broad IEA.

- term:
    id: GO:2000303
    label: regulation of ceramide biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA from ARBA for regulation of ceramide biosynthetic process. This is
      correct but could be more specific: ORMDL3 is a negative regulator, and
      the more specific child term GO:1900060 (negative regulation of ceramide
      biosynthetic process) is already annotated via IMP.
    action: ACCEPT
    reason: >-
      Correct at the level of specificity typical for IEA. The more precise
      negative regulation term (GO:1900060) is captured by the IMP annotation
      from PMID:25691431.

# --- Protein binding annotations (IPI) ---
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20182505
  review:
    summary: >-
      Physical interaction between ORMDL3 and SPTLC1 (O15269) demonstrated by
      co-immunoprecipitation from HEK293T cells expressing 3xFlag-tagged
      ORMDL3 (PMID:20182505). This interaction is functionally significant as
      ORMDL3 is a regulatory subunit of the SPT complex.
    action: MODIFY
    reason: >-
      The protein binding annotation is uninformative. The interaction with
      SPTLC1 reflects ORMDL3's role as a subunit of the SPT complex. A more
      informative annotation would be enzyme inhibitor activity (GO:0004857),
      reflecting ORMDL3's function as a direct inhibitor of SPT catalytic
      activity through physical interaction.
    proposed_replacement_terms:
    - id: GO:0004857
      label: enzyme inhibitor activity
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        Immunoprecipitations from HEK293T cells expressing 3×Flag-tagged Ormdl3
        led to a prominent Sptlc1 band detected by Western blot (Fig

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: >-
      High-throughput binary protein interactome study (HuRI) reporting many
      interactions for ORMDL3. Most of these interactions (with AQP6, ARL13B,
      various GPCRs, channels, etc.) lack functional validation and likely
      represent the promiscuous detection typical of membrane protein screens.
      The biologically meaningful interactions are with SPT complex components,
      not with the diverse set of membrane proteins identified here.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      High-throughput interactome data. The 25+ distinct interactors from this
      single study include many membrane proteins with no known functional
      relationship to ORMDL3 (e.g., AQP6, GPR101, GPR152, ROM1). Generic
      protein binding from HT screens is uninformative for ORMDL3's function.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: >-
        Here we present a human 'all-by-all' reference interactome map of human
        binary protein interactions, or 'HuRI'. With approximately 53,000
        protein-protein interactions

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33558761
  review:
    summary: >-
      Cryo-EM structure of the human SPT-ORMDL3 complex at 2.6 Angstrom
      resolution demonstrates direct physical contact between ORMDL3 and SPTLC1
      (O15269) within the SPT holoenzyme (PMID:33558761). This is structurally
      validated interaction, not mere binding.
    action: MODIFY
    reason: >-
      The protein binding term is uninformative. The structural data reveal
      that ORMDL3 physically occludes the SPT substrate entry tunnel, acting as
      an enzyme inhibitor. This should be annotated as enzyme inhibitor activity.
    proposed_replacement_terms:
    - id: GO:0004857
      label: enzyme inhibitor activity
    supported_by:
    - reference_id: PMID:33558761
      supporting_text: >-
        ORMDL3 blocks the tunnel and competes with substrate binding through
        its amino terminus

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33558762
  review:
    summary: >-
      Second independent cryo-EM structure study of the SPT-ORMDL3 complex
      (Li et al. 2021) confirming physical interaction between ORMDL3 and
      SPTLC1 within the SPT holoenzyme at 3.2 Angstrom resolution.
    action: MODIFY
    reason: >-
      As with PMID:33558761, the generic protein binding annotation is
      uninformative. The structural interaction represents enzyme inhibitor
      activity within the SPT complex.
    proposed_replacement_terms:
    - id: GO:0004857
      label: enzyme inhibitor activity
    supported_by:
    - reference_id: PMID:33558762
      supporting_text: >-
        ORMDL3 is located in the center of the complex, serving to stabilize
        the SPT assembly

# --- IDA annotations ---
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: >-
      IDA annotation from HPA immunofluorescence data. ORMDL3 localizes to the
      ER, consistent with its known ER membrane topology and function as an SPT
      complex subunit.
    action: ACCEPT
    reason: >-
      Correct. ER localization is the primary subcellular localization of
      ORMDL3, confirmed by multiple methods including GFP-fusion (PMID:12093374),
      immunofluorescence (PMID:19819884), and cryo-EM structures.

# --- Annotations from PMID:28747345 (Dang et al. 2017, B cell autophagy) ---
- term:
    id: GO:0002903
    label: negative regulation of B cell apoptotic process
  evidence_type: IMP
  original_reference_id: PMID:28747345
  review:
    summary: >-
      Dang et al. 2017 showed that Ormdl3 knockout mice have increased
      apoptosis of splenic B cells, and that ORMDL3 facilitates B cell survival
      via ATF6-Beclin1 autophagy pathway. The annotation reflects a downstream
      phenotypic consequence in the immune system.
    action: KEEP_AS_NON_CORE
    reason: >-
      This is a pleiotropic downstream effect likely mediated through ORMDL3's
      primary role in sphingolipid/ER stress regulation, rather than a direct
      molecular function of ORMDL3 in anti-apoptotic signaling. B cell survival
      effects are likely secondary to altered sphingolipid metabolism and ER
      stress responses.
    supported_by:
    - reference_id: PMID:28747345
      supporting_text: >-
        silencing Ormdl3 in vivo significantly decreased the proportions of
        mature B lymphocytes and transitional 2B cells in spleen... knockdown
        of Ormdl3 augmented the apoptosis of total splenic cells and splenic
        CD19+ B cells

- term:
    id: GO:0010508
    label: positive regulation of autophagy
  evidence_type: IDA
  original_reference_id: PMID:28747345
  review:
    summary: >-
      Dang et al. 2017 showed ORMDL3 promotes autophagy via the ATF6-Beclin1
      pathway. ORMDL3 overexpression increased Beclin1 and LC3-II expression
      and increased autophagy marker levels. This likely reflects secondary
      effects of ORMDL3's role in ER stress modulation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Autophagy regulation by ORMDL3 appears to be an indirect consequence of
      its effects on ER stress/UPR signaling (ATF6 activation), which itself
      may stem from altered sphingolipid metabolism. This is not a core
      molecular function.
    supported_by:
    - reference_id: PMID:28747345
      supporting_text: >-
        ORMDL3 potentially mediates the autophagy via the ATF 6-Beclin1
        autophagy pathway, and it facilitates the survival of splenic B cells
        via promoting autophagy and suppressing apoptosis

- term:
    id: GO:0010508
    label: positive regulation of autophagy
  evidence_type: IMP
  original_reference_id: PMID:28747345
  review:
    summary: >-
      Duplicate annotation for positive regulation of autophagy with IMP
      evidence from the same study. Ormdl3 knockout in mice showed reduced
      autophagy markers in splenic B cells.
    action: KEEP_AS_NON_CORE
    reason: >-
      Same rationale as the IDA annotation above. Autophagy regulation is a
      downstream pleiotropic effect of ORMDL3's primary sphingolipid regulatory
      function, not a core molecular activity.
    supported_by:
    - reference_id: PMID:28747345
      supporting_text: >-
        ORMDL3 potentially mediates the autophagy via the ATF 6-Beclin1
        autophagy pathway, and it facilitates the survival of splenic B cells
        via promoting autophagy and suppressing apoptosis

- term:
    id: GO:1900182
    label: positive regulation of protein localization to nucleus
  evidence_type: IDA
  original_reference_id: PMID:28747345
  review:
    summary: >-
      Dang et al. 2017 reported that ORMDL3 promotes nuclear localization of
      ATF6 (a UPR transcription factor). This likely reflects ORMDL3's effects
      on ER stress signaling through sphingolipid metabolism, not a direct
      protein transport function.
    action: KEEP_AS_NON_CORE
    reason: >-
      The positive regulation of protein localization to nucleus annotation
      appears to refer to ATF6 nuclear translocation as part of the UPR. This
      is an indirect downstream effect of ORMDL3's sphingolipid regulatory
      function, not a core activity.
    supported_by:
    - reference_id: PMID:28747345
      supporting_text: >-
        we uncovered a role of ORMDL3 in fine-tuning B cell development and
        survival, besides highlighting a potential mechanism by which ORMDL3
        regulates autophagy via ATF6 pathway

# --- Reactome TAS annotations ---
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6798743
  review:
    summary: >-
      Reactome annotation placing ORMDL3 at the plasma membrane based on
      neutrophil degranulation pathway. ORMDL3 is an ER-resident protein with
      no experimental evidence for plasma membrane localization. The original
      discovery paper (PMID:12093374) explicitly showed no colocalization with
      plasma membrane markers.
    action: REMOVE
    reason: >-
      ORMDL3 is established as an ER-resident multi-pass transmembrane protein.
      Hjelmqvist et al. 2002 showed that EGFP-ORMDL3 colocalizes with the ER
      marker PDI but showed no overlapping signal with plasma membrane marker
      concanavalin A. The Reactome pathway for neutrophil degranulation may
      include ORMDL3 based on proteomics of secretory granule fractions, but
      this does not represent the functional localization of ORMDL3.
    supported_by:
    - reference_id: PMID:12093374
      supporting_text: >-
        double-label fluorescence with biotin-labeled concanavalin A... showed
        no overlapping signal with EGFP-ORMDL at the plasmatic membrane

- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6799350
  review:
    summary: >-
      Second Reactome annotation to plasma membrane from specific granule
      exocytosis pathway. Same issue as above.
    action: REMOVE
    reason: >-
      No experimental evidence supports plasma membrane localization of ORMDL3.
      ORMDL3 is firmly established as an ER membrane protein by GFP-fusion,
      immunofluorescence, and cryo-EM structural studies.

- term:
    id: GO:0030667
    label: secretory granule membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6798743
  review:
    summary: >-
      Reactome annotation placing ORMDL3 in secretory granule membranes from
      the neutrophil degranulation pathway. While ORMDL3 may have been detected
      in proteomics of granule fractions, its established function and
      localization is in the ER as part of the SPT complex.
    action: REMOVE
    reason: >-
      ORMDL3's confirmed localization and functional site is the ER membrane.
      Detection in granule proteomic fractions may reflect ER contamination or
      transit through the secretory pathway, not a functional localization.

- term:
    id: GO:0035579
    label: specific granule membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6799350
  review:
    summary: >-
      Reactome annotation to specific granule membrane from neutrophil-specific
      granule exocytosis pathway. Same concern as secretory granule membrane.
    action: REMOVE
    reason: >-
      No functional evidence supports ORMDL3 localization to specific granule
      membranes. This likely arises from proteomic detection in granule
      fractions that may include ER membrane contaminants.

# --- IDA/IMP annotations from PMID:25691431 (Siow et al. 2015) ---
- term:
    id: GO:0017059
    label: serine palmitoyltransferase complex
  evidence_type: IDA
  original_reference_id: PMID:25691431
  review:
    summary: >-
      Siow et al. 2015 demonstrated that ORMDLs and SPT form stable complexes
      in human bronchial epithelial cells (HBECs) and HeLa cells, and that
      ORMDL is expressed in functional excess relative to SPT. Direct
      experimental evidence for SPT complex membership.
    action: ACCEPT
    reason: >-
      Core localization. Direct biochemical evidence for ORMDL3 as a component
      of the SPT complex in human cells.
    supported_by:
    - reference_id: PMID:25691431
      supporting_text: >-
        ORMDLs and SPT form stable complexes that are not increased by elevated
        ORMDL3 expression

- term:
    id: GO:1900060
    label: negative regulation of ceramide biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:25691431
  review:
    summary: >-
      Siow et al. 2015 showed that ORMDL3 negatively regulates ceramide
      biosynthesis, though the relationship is complex due to ORMDL
      stoichiometry with SPT. At normal expression levels, ORMDL is in
      functional excess over SPT, meaning additional ORMDL3 does not further
      suppress biosynthesis.
    action: ACCEPT
    reason: >-
      Core function. ORMDL3's role as a negative regulator of ceramide
      biosynthesis (via SPT inhibition) is well established. This is the most
      specific biological process term available for ORMDL3's primary function.
    supported_by:
    - reference_id: PMID:25691431
      supporting_text: >-
        The ORM1 (Saccharomyces cerevisiae)-like proteins (ORMDLs) and their
        yeast orthologs, the Orms, are negative homeostatic regulators of the
        initiating enzyme in sphingolipid biosynthesis, serine
        palmitoyltransferase (SPT)

# --- IDA annotations from PMID:12093374 and PMID:20182505 ---
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:12093374
  review:
    summary: >-
      Original characterization of the ORMDL gene family by Hjelmqvist et al.
      2002. GFP-ORMDL3 fusion protein colocalized with the ER marker PDI in
      COS-7 cells by confocal microscopy, establishing ER localization.
    action: ACCEPT
    reason: >-
      Primary experimental evidence for ER localization of ORMDL3. This is the
      foundational study establishing the subcellular localization of the ORMDL
      protein family.
    supported_by:
    - reference_id: PMID:12093374
      supporting_text: >-
        Confocal scanning microscopy using an antibody against
        protein-disulfide isomerase (PDI), an ER-marker protein, showed an
        overlapping signal in the endoplasmic reticulum... these data show that
        the ORMDL proteins locate at the ER membrane

- term:
    id: GO:0006672
    label: ceramide metabolic process
  evidence_type: IMP
  original_reference_id: PMID:20182505
  review:
    summary: >-
      Breslow et al. 2010 demonstrated that simultaneous RNAi knockdown of
      ORMDL1/2/3 in HeLa cells causes approximately three-fold increase in
      ceramide levels. This landmark study established the role of ORM/ORMDL
      proteins in sphingolipid homeostasis.
    action: ACCEPT
    reason: >-
      Core function. Direct experimental evidence that ORMDL proteins regulate
      ceramide levels in human cells.
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        we found that simultaneous knock-down by RNAi of ORMDL1/2/3 in Hela
        cells causes an approximately three-fold increase in ceramide levels

- term:
    id: GO:0017059
    label: serine palmitoyltransferase complex
  evidence_type: IDA
  original_reference_id: PMID:20182505
  review:
    summary: >-
      Breslow et al. 2010 showed that Flag-tagged ORMDL3 co-immunoprecipitates
      with SPTLC1 from HEK293T cells, demonstrating the conserved physical
      association between ORMDL3 and the SPT complex in human cells.
    action: ACCEPT
    reason: >-
      Core localization. Direct co-IP evidence for ORMDL3 as a component of
      the SPT complex in human cells, confirmed by subsequent cryo-EM
      structures.
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        Immunoprecipitations from HEK293T cells expressing 3×Flag-tagged Ormdl3
        led to a prominent Sptlc1 band detected by Western blot (Fig

# --- NEW annotations suggested ---
- term:
    id: GO:0004857
    label: enzyme inhibitor activity
  evidence_type: IDA
  original_reference_id: PMID:33558761
  review:
    summary: >-
      ORMDL3 functions as a direct inhibitor of the SPT enzyme by physically
      occluding the substrate entry tunnel through its N-terminus. Cryo-EM
      structures at 2.6 Angstrom resolution show that ORMDL3 blocks the
      substrate-binding tunnel and competes with substrate binding. This is the
      primary molecular function of ORMDL3.
    action: NEW
    reason: >-
      ORMDL3 has no MF annotation other than the uninformative protein binding.
      The structural and biochemical evidence clearly demonstrates that ORMDL3
      functions as an enzyme inhibitor of SPT. This is the core molecular
      function of the protein.
    supported_by:
    - reference_id: PMID:33558761
      supporting_text: >-
        ORMDL3 blocks the tunnel and competes with substrate binding through
        its amino terminus
    - reference_id: PMID:20182505
      supporting_text: >-
        we identify Orm proteins as negative regulators of sphingolipid
        synthesis that form a conserved complex with serine
        palmitoyltransferase, the first and rate-limiting enzyme in
        sphingolipid production

- term:
    id: GO:0097001
    label: ceramide binding
  evidence_type: IDA
  original_reference_id: PMID:37308477
  review:
    summary: >-
      Xie et al. 2023 demonstrated that ceramide binds to the N-terminus of
      ORMDL3, stabilizing an inhibitory conformation. Key residue Asn13 is
      critical for ceramide binding; N13A mutation disrupts ceramide
      responsiveness. Cryo-EM structures resolved the ceramide-bound SPT-ORMDL3
      complex.
    action: NEW
    reason: >-
      Ceramide binding is a critical molecular function of ORMDL3 that enables
      the homeostatic feedback loop. This is structurally and mutagenetically
      validated and represents a genuine molecular function annotation.
    additional_reference_ids:
    - PMID:37308477
    supported_by:
    - reference_id: PMID:37308477
      supporting_text: >-
        purified human SPT-ORMDL complexes are inhibited by the central
        sphingolipid metabolite ceramide. We have solved the cryo-EM structure
        of the SPT-ORMDL3 complex in a ceramide-bound state. Structure-guided
        mutational analyses reveal the essential function of this ceramide
        binding site for the suppression of SPT activity.

- term:
    id: GO:0090155
    label: negative regulation of sphingolipid biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:20182505
  review:
    summary: >-
      Breslow et al. 2010 established that ORM/ORMDL proteins are negative
      regulators of sphingolipid biosynthesis. RNAi knockdown of all three
      ORMDL genes in HeLa cells increased ceramide levels three-fold,
      demonstrating the negative regulatory role. This term captures the
      specific directionality of ORMDL3's regulatory function better than the
      more general terms currently annotated.
    action: NEW
    reason: >-
      This term specifically captures ORMDL3's role as a negative regulator of
      sphingolipid biosynthesis, which is more precise than the existing
      GO:0030148 (sphingolipid biosynthetic process) annotation. The current
      GO annotations lack a biological process term that specifies the negative
      regulatory direction.
    supported_by:
    - reference_id: PMID:20182505
      supporting_text: >-
        we identify Orm proteins as negative regulators of sphingolipid
        synthesis that form a conserved complex with serine
        palmitoyltransferase

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:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning 
    models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:12093374
  title: ORMDL proteins are a conserved new family of endoplasmic reticulum 
    membrane proteins.
  findings:
  - statement: >-
      ORMDL3 encodes a 153 amino acid ER-resident transmembrane protein.
      GFP-ORMDL3 colocalizes with ER marker PDI but not with plasma membrane
      marker concanavalin A in COS-7 cells. Human ORMDL3 can rescue yeast
      orm1/orm2 double knockout phenotypes, demonstrating functional
      conservation.
    supporting_text: >-
      Confocal scanning microscopy using an antibody against protein-disulfide
      isomerase (PDI), an ER-marker protein, showed an overlapping signal in
      the endoplasmic reticulum
- id: PMID:20182505
  title: Orm family proteins mediate sphingolipid homeostasis.
  findings:
  - statement: >-
      Landmark study identifying ORM/ORMDL proteins as negative regulators of
      SPT that form a conserved complex (SPOTS complex) with SPT and Sac1.
      ORMDL3 co-immunoprecipitates with SPTLC1 in human HEK293T cells.
      Triple RNAi knockdown of ORMDL1/2/3 in HeLa cells increases ceramide
      levels ~3-fold.
    supporting_text: >-
      we found that simultaneous knock-down by RNAi of ORMDL1/2/3 in Hela
      cells causes an approximately three-fold increase in ceramide levels
- id: PMID:25691431
  title: ORMDL/serine palmitoyltransferase stoichiometry determines effects of 
    ORMDL3 expression on sphingolipid biosynthesis.
  findings:
  - statement: >-
      ORMDLs and SPT form stable complexes in human cells. ORMDL is normally
      expressed in functional excess relative to SPT, meaning ORMDL3
      overexpression does not further suppress biosynthesis. The relationship
      between ORMDL3 expression and sphingolipid levels is complex and
      stoichiometry-dependent.
    supporting_text: >-
      We determined that ORMDL is expressed in functional excess relative to
      SPT at normal levels of expression. ORMDLs and SPT form stable complexes
      that are not increased by elevated ORMDL3 expression.
- id: PMID:28747345
  title: "ORMDL3 Facilitates the Survival of Splenic B Cells via an ATF6α-Endoplasmic
    Reticulum Stress-Beclin1 Autophagy Regulatory Pathway."
  findings:
  - statement: >-
      ORMDL3 knockout in mice decreases mature B cells, increases splenic B cell
      apoptosis, and reduces autophagy. ORMDL3 promotes B cell survival via
      ATF6-Beclin1 autophagy pathway. These are likely downstream effects of
      altered sphingolipid metabolism and ER stress.
    supporting_text: >-
      silencing Ormdl3 in vivo significantly decreased the proportions of
      mature B lymphocytes and transitional 2B cells in spleen
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings:
  - statement: >-
      High-throughput binary protein interactome mapping study (HuRI). Reports
      many ORMDL3 interactors but most are unvalidated membrane protein
      interactions from yeast two-hybrid screens.
    supporting_text: >-
      Here we present a human 'all-by-all' reference interactome map of human
      binary protein interactions, or 'HuRI'. With approximately 53,000
      protein-protein interactions
- id: PMID:33558761
  title: Structural insights into the regulation of human serine 
    palmitoyltransferase complexes.
  findings:
  - statement: >-
      Cryo-EM structures of the human SPT-ORMDL3 complex at 2.6-3.4 Angstrom
      resolution. Reveals that ORMDL3 blocks the SPT substrate-binding tunnel
      through its N-terminus, competing with substrate binding. ssSPTa shapes
      the tunnel to determine substrate specificity.
    supporting_text: >-
      ORMDL3 blocks the tunnel and competes with substrate binding through
      its amino terminus
- id: PMID:33558762
  title: Structural insights into the assembly and substrate selectivity of 
    human SPT-ORMDL3 complex.
  findings:
  - statement: >-
      Independent cryo-EM structures of the human SPT-ORMDL3 complex at 3.2
      Angstrom resolution confirming the four-transmembrane topology of ORMDL3
      and its integration within the SPT holoenzyme.
    supporting_text: >-
      ORMDL3 is located in the center of the complex, serving to stabilize
      the SPT assembly
- id: PMID:37308477
  title: Ceramide sensing by human SPT-ORMDL complex for establishing 
    sphingolipid homeostasis.
  findings:
  - statement: >-
      Cryo-EM structures and mutagenesis demonstrating that ceramide binds to
      the ORMDL3 N-terminus and stabilizes the inhibitory conformation that
      blocks SPT activity. Key residue Asn13 is essential for ceramide sensing.
    supporting_text: >-
      Structural studies indicate that ceramide can induce and lock the
      N-terminus of ORMDL3 into an inhibitory conformation.
- id: PMID:30700557
  title: "The ORMDL/Orm-serine palmitoyltransferase (SPT) complex is directly regulated by ceramide: Reconstitution of SPT regulation in isolated membranes."
  findings:
  - statement: >-
      Reconstitution of SPT regulation in isolated membranes demonstrates that
      ceramide directly regulates the ORMDL/SPT complex, providing biochemical
      evidence for the ceramide feedback mechanism.
    supporting_text: >-
      Sphingolipid and ORMDL-dependent regulation of SPT was demonstrated in
      isolated membranes, essentially free of cytosol. This suggests that this
      regulation does not require soluble cytosolic proteins or small molecules
      such as ATP. We found that this system is particularly responsive to the
      pro-apoptotic sphingolipid ceramide
- id: Reactome:R-HSA-6798743
  title: Exocytosis of secretory granule membrane proteins
  findings: []
- id: Reactome:R-HSA-6799350
  title: Exocytosis of specific granule membrane proteins
  findings: []
- id: file:human/ORMDL3/ORMDL3-deep-research-falcon.md
  title: Deep research review of ORMDL3 function
  findings:
  - statement: >-
      Comprehensive literature review covering ORMDL3 as ER-resident SPT
      regulator, ceramide-dependent feedback mechanism, roles in asthma,
      immune cell biology, ER stress/UPR, and innate immunity.

core_functions:
- description: >-
    Negative regulation of serine palmitoyltransferase (SPT) activity as a
    ceramide-sensitive regulatory subunit of the SPT holoenzyme complex.
    ORMDL3 physically occludes the SPT substrate entry tunnel through its
    N-terminus, competing with substrate binding (PMID:33558761). Ceramide
    binding to the ORMDL3 N-terminus (Asn13-dependent) stabilizes this
    inhibitory conformation, implementing homeostatic feedback control of
    de novo sphingolipid biosynthesis (PMID:37308477).
  molecular_function:
    id: GO:0004857
    label: enzyme inhibitor activity
  supported_by:
  - reference_id: PMID:20182505
    supporting_text: >-
      we identify Orm proteins as negative regulators of sphingolipid
      synthesis that form a conserved complex with serine
      palmitoyltransferase, the first and rate-limiting enzyme in
      sphingolipid production
  - reference_id: PMID:33558761
    supporting_text: >-
      ORMDL3 blocks the tunnel and competes with substrate binding through
      its amino terminus
  - reference_id: PMID:37308477
    supporting_text: >-
      Ceramide sensing by human SPT-ORMDL complex for establishing
      sphingolipid homeostasis

- description: >-
    Ceramide binding at the N-terminus enabling homeostatic feedback
    regulation of sphingolipid de novo biosynthesis. ORMDL3 senses
    cellular ceramide levels and translates this into inhibition of SPT
    activity. Asn13 is a critical residue for ceramide sensing
    (PMID:37308477). This molecular sensing function is integral to the
    sphingolipid homeostatic feedback loop.
  molecular_function:
    id: GO:0097001
    label: ceramide binding
  supported_by:
  - reference_id: PMID:37308477
    supporting_text: >-
      Structural studies indicate that ceramide can induce and lock the
      N-terminus of ORMDL3 into an inhibitory conformation.
  - reference_id: PMID:30700557
    supporting_text: >-
      The ORMDL/Orm-serine palmitoyltransferase (SPT) complex is directly
      regulated by ceramide [reconstitution demonstrates direct ceramide
      regulation of the ORMDL/SPT complex]
    full_text_unavailable: true