CRTAP (cartilage-associated protein) is an endoplasmic reticulum (ER) lumen glycoprotein that is an essential, non-catalytic subunit of the collagen prolyl 3-hydroxylation complex, together with prolyl 3-hydroxylase 1 (P3H1/LEPRE1) and cyclophilin B (PPIB/CyPB). Within this ternary complex, P3H1 provides the catalytic prolyl 3-hydroxylase activity and PPIB the peptidyl-prolyl cis-trans isomerase activity, while CRTAP acts as a scaffolding/helper subunit required for complex assembly and stability. The complex 3-hydroxylates a single specific proline residue (Pro986) of the alpha1(I) and alpha1(II) fibrillar procollagen chains in the ER and also functions as a collagen-specific molecular chaperone/foldase that controls the rate of collagen triple-helix folding; delayed folding in its absence leads to overmodification of the collagen helix. CRTAP and P3H1 are mutually stabilizing: loss of either protein destabilizes the other. A minor fraction of CRTAP is secreted into the extracellular space/matrix. Biallelic loss-of-function variants cause autosomal recessive osteogenesis imperfecta type VII, underscoring an essential role in collagen biosynthesis and skeletal development.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005518 collagen binding | IBA GO_REF:0000033 | ACCEPT | Summary: The collagen prolyl 3-hydroxylation complex binds fibrillar (pro)collagen as substrate, and cryo-EM shows CRTAP contributes to a multi-site collagen substrate-interacting zone within the P3H1/CRTAP/PPIB complex. The contributes_to qualifier is appropriate because substrate binding is a property of the assembled complex rather than CRTAP alone. Reason: Supported by structural evidence that CRTAP forms part of the collagen substrate-interacting surface of the complex; contributes_to qualifier is biologically accurate for an accessory subunit. Supporting Evidence: PMID:39245686 The structure of the P3H1/CRTAP/PPIB/collagen peptide complex reveals multiple binding sites, suggesting a substrate interacting zone. |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: CRTAP is active in the ER, where the prolyl 3-hydroxylation complex modifies and chaperones procollagen. This IBA agrees with direct experimental localization, though the more precise term is ER lumen. Reason: ER is the validated functional compartment; consistent with IDA evidence and the ER-lumen Reactome annotations. Supporting Evidence: PMID:19846465 CRTAP and P3H1 form a complex with cyclophilin B (CyPB) in the endoplasmic reticulum (ER) which 3-hydroxylates the Pro986 residue of alpha1(I) and alpha1(II) collagen chains. |
| GO:0030199 collagen fibril organization | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Loss of the complex delays collagen folding and causes overmodified collagen with disorganized matrix; the complex also modulates type I collagen fibril formation in vitro. CRTAP is therefore reasonably annotated to collagen fibril organization, though this is a downstream/structural consequence rather than CRTAP's direct molecular activity. Reason: Supported but indirect; the core function is ER collagen 3-hydroxylation and chaperoning, with fibril organization being a downstream effect. Supporting Evidence: PMID:19846465 function as a chaperone in both classical chaperone assays inhibiting citrate synthase aggregation and rhodanese refolding and aggregation, as well as in a fibril formation assay of type I collagen |
| GO:0005515 protein binding | IPI PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Ma... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from a high-throughput crosslinking-MS study. The WITH/FROM is P3H1 (UniProtKB:Q32P28), so the meaningful content is the CRTAP-P3H1 interaction, captured more specifically by complex membership. Reason: Uninformative bare protein binding term; the specific, biologically relevant interaction (CRTAP-P3H1 within the prolyl 3-hydroxylation complex) is better represented by complex-membership annotations. Supporting Evidence: PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Bare protein binding from the BioPlex affinity-purification MS interactome. The WITH/FROM is P3H1 (UniProtKB:Q32P28), reflecting the CRTAP-P3H1 interaction, which is better captured by complex membership. Reason: Uninformative bare protein binding term from a high-throughput dataset; the specific interaction with P3H1 is represented by complex-membership and core function annotations. Supporting Evidence: PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000120 | ACCEPT | Summary: Automated electronic annotation of ER localization, redundant with but consistent with the experimental IDA and IBA ER annotations for this gene. Reason: Correct ER location, the validated functional compartment; consistent with the experimental IDA evidence for this gene. Supporting Evidence: PMID:19846465 CRTAP and P3H1 form a complex with cyclophilin B (CyPB) in the endoplasmic reticulum (ER) |
| GO:0007283 spermatogenesis | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Electronic transfer from a mouse ortholog (UniProtKB:Q9CYD3) via Ensembl Compara. There is no human experimental evidence linking CRTAP to spermatogenesis, and the established core biology is ER collagen modification and skeletal connective tissue. Reason: Broad ortholog-transfer annotation lacking human evidence and unrelated to the validated collagen-modification/chaperone function of CRTAP. Supporting Evidence: GO_REF:0000107 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara |
| GO:0005515 protein binding | IPI PMID:39245686 The structural basis for the collagen processing by human P3... | MARK AS OVER ANNOTATED | Summary: Bare protein binding term, but here supported by direct cryo-EM structural evidence of the P3H1/CRTAP/PPIB ternary complex (WITH/FROM P3H1, UniProtKB:Q32P28). The specific, informative content is complex membership / the CRTAP-P3H1 interaction rather than generic protein binding. Reason: Bare protein binding is uninformative; the underlying structural finding is best represented by the prolyl 3-hydroxylation complex membership and the collagen-substrate-binding core function. Supporting Evidence: PMID:39245686 We determine cryo-EM structures of the P3H1/CRTAP/PPIB complex. |
| GO:0050821 protein stabilization | IMP PMID:19846465 Prolyl 3-hydroxylase 1 and CRTAP are mutually stabilizing in... | ACCEPT | Summary: CRTAP stabilizes P3H1 in the ER: null mutation in either gene causes loss or substantial reduction of both proteins despite normal partner transcript levels, and proteasome inhibition partially rescues P3H1 in CRTAP-null cells. This is a genuine, experimentally demonstrated function (mutual stabilization of complex subunits). Reason: Directly demonstrated by IMP in patient fibroblasts; CRTAP stabilizes its complex partner P3H1, a core aspect of complex assembly and integrity. Supporting Evidence: PMID:19846465 These data indicate that CRTAP and P3H1 are mutually stabilized in the collagen prolyl 3-hydroxylation complex. |
| GO:0006457 protein folding | ISS GO_REF:0000024 | MODIFY | Summary: The prolyl 3-hydroxylation complex acts as a collagen-specific molecular chaperone/foldase; absence of CRTAP delays collagen helix folding. Protein folding is supported but generic; a more specific term such as protein folding in endoplasmic reticulum better captures the biology. Reason: Supported chaperone/foldase activity, but the generic protein folding term can be made more precise to reflect the ER collagen-folding role. Proposed replacements: protein folding in endoplasmic reticulum Supporting Evidence: PMID:20089953 In the absence of P3H1 or CRTAP, alpha1(I)Pro986 3-hydroxylation is decreased and collagen folding is delayed, resulting in overmodification of the helical lysine and proline residues. |
| GO:0032991 protein-containing complex | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: CRTAP is part of the heterotrimeric P3H1/CRTAP/PPIB collagen prolyl 3-hydroxylation complex, now confirmed by cryo-EM. The generic protein-containing complex term is correct but uninformative about which complex; it is retained as the most specific validated CC complex term available in the existing annotation set. Reason: Correct but generic; complex membership in the specific prolyl 3-hydroxylation complex is captured in core_functions (in_complex). Supporting Evidence: PMID:39245686 We determine cryo-EM structures of the P3H1/CRTAP/PPIB complex. |
| GO:0005783 endoplasmic reticulum | IDA PMID:20089953 Lack of cyclophilin B in osteogenesis imperfecta with normal... | ACCEPT | Summary: Direct immunofluorescence localization of endogenous CRTAP to the ER in human fibroblasts. This is strong, primary evidence for the core ER location. Reason: Direct experimental localization to the ER, the validated functional compartment for CRTAP. Supporting Evidence: PMID:20089953 Cells from the proband and a 5-year-old control subject were stained with antibodies to CyPB, P3H1, CRTAP ... to examine protein colocalization by means of confocal microscopy. |
| GO:0005576 extracellular region | IDA PMID:19846465 Prolyl 3-hydroxylase 1 and CRTAP are mutually stabilizing in... | KEEP AS NON CORE | Summary: A minor fraction of CRTAP is secreted (~10-12% in normal cells, rising to 15-20% when its ER-retention partner P3H1 is absent). Secretion is real but represents a small, secondary pool; the dominant biology is ER-luminal. Reason: Experimentally observed secreted pool, but a minor fraction relative to the ER-resident function; not a core localization. Supporting Evidence: PMID:19846465 in conditioned media from control cells ... about 10-12% of total CRTAP is secreted |
| GO:0005783 endoplasmic reticulum | IDA PMID:19846465 Prolyl 3-hydroxylase 1 and CRTAP are mutually stabilizing in... | ACCEPT | Summary: Direct localization of CRTAP to the ER by immunofluorescence in patient and control fibroblasts, consistent with its role in the ER prolyl 3-hydroxylation complex. Reason: Direct experimental evidence for the core ER location of CRTAP. Supporting Evidence: PMID:19846465 CRTAP and P3H1 form a complex with cyclophilin B (CyPB) in the endoplasmic reticulum (ER) |
| GO:1901874 negative regulation of post-translational protein modification | IMP PMID:19846465 Prolyl 3-hydroxylase 1 and CRTAP are mutually stabilizing in... | KEEP AS NON CORE | Summary: This annotation reflects that loss of the complex causes overmodification (excess 4-hydroxylation and lysyl hydroxylation) of the collagen helix; i.e., the complex normally limits overmodification by controlling folding rate. This is an indirect consequence of the chaperone/foldase activity rather than a direct regulatory function of CRTAP on a modifying enzyme. Reason: Supported as an indirect/consequential phenotype of delayed-folding prevention; not a direct molecular regulatory function of CRTAP. Supporting Evidence: PMID:19846465 Excess modification, or 'overmodification' of the collagen helix can be detected as delayed electrophoretic migration of collagen alpha chains |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-1980233 | ACCEPT | Summary: Reactome localizes CRTAP to the ER lumen, the precise compartment where the prolyl 3-hydroxylation complex acts on procollagen. This is more specific than the generic ER term and is well supported. Reason: Accurate and more precise than endoplasmic reticulum; the ER lumen is the validated site of complex activity. Supporting Evidence: PMID:19846465 CRTAP and P3H1 form a complex with cyclophilin B (CyPB) in the endoplasmic reticulum (ER) which 3-hydroxylates the Pro986 residue |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-2022073 | ACCEPT | Summary: Redundant Reactome ER-lumen localization (procollagen triple helix formation reaction). Correct and consistent with the validated ER-luminal location. Reason: Correct, precise ER-lumen location consistent with the accepted ER-lumen annotation; retained as a redundant but valid localization. Supporting Evidence: PMID:39245686 the modifications of proline residues play critical roles in the formation of triple helix and the maintenance of stability |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-8948226 | ACCEPT | Summary: Redundant Reactome ER-lumen localization (prolyl 3-hydroxylase complex dissociation reaction). Correct location, consistent with the accepted ER-lumen annotation. Reason: Correct, precise ER-lumen location consistent with the accepted ER-lumen annotation; retained as a redundant but valid localization. Supporting Evidence: PMID:19846465 the collagen prolyl 3-hydroxylation complex in the endoplasmic reticulum (ER) |
| GO:0005788 endoplasmic reticulum lumen | TAS Reactome:R-HSA-8948230 | ACCEPT | Summary: Redundant Reactome ER-lumen localization (P3HB binds 4-Hyp-collagen propeptides reaction). Correct location, consistent with the accepted ER-lumen annotation. Reason: Correct, precise ER-lumen location consistent with the accepted ER-lumen annotation; retained as a redundant but valid localization. Supporting Evidence: PMID:19846465 the collagen prolyl 3-hydroxylation complex in the endoplasmic reticulum (ER) |
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Download this section (compressed HTML)Q: Is there a GO cellular component term specifically for the collagen prolyl 3-hydroxylation (P3H1/CRTAP/PPIB) complex, and if not should one be created so CRTAP can be annotated more specifically than protein-containing complex?
Q: Does CRTAP have any chaperone or substrate-binding function independent of P3H1 and PPIB, given that the proteins are mutually stabilizing and largely co-dependent?
Experiment: Reconstitute the P3H1/CRTAP/PPIB complex and assay prolyl 3-hydroxylase activity and collagen-folding (chaperone/foldase) activity with and without CRTAP to quantify CRTAP's specific contribution to catalysis versus substrate binding and folding.
Experiment: Map the CRTAP residues that form the collagen substrate-interacting zone (from the cryo-EM model) by structure-guided mutagenesis, and test effects on Pro986 3-hydroxylation efficiency and collagen folding rate in cells.
Experiment: Use proximity labeling (BioID/APEX) of CRTAP in osteoblasts/chondrocytes to define its ER interactome and any partners beyond P3H1/PPIB that participate in collagen maturation.
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