id: O75718 gene_symbol: CRTAP product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- 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. existing_annotations: - term: id: GO:0005518 label: collagen binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: contributes_to review: 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. action: ACCEPT 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. supported_by: - reference_id: PMID:39245686 supporting_text: >- The structure of the P3H1/CRTAP/PPIB/collagen peptide complex reveals multiple binding sites, suggesting a substrate interacting zone. - term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: 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. action: ACCEPT reason: >- ER is the validated functional compartment; consistent with IDA evidence and the ER-lumen Reactome annotations. supported_by: - reference_id: PMID:19846465 supporting_text: >- 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. - term: id: GO:0030199 label: collagen fibril organization evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: 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. action: KEEP_AS_NON_CORE reason: >- Supported but indirect; the core function is ER collagen 3-hydroxylation and chaperoning, with fibril organization being a downstream effect. supported_by: - reference_id: PMID:19846465 supporting_text: >- 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 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:30021884 qualifier: enables review: 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. action: MARK_AS_OVER_ANNOTATED 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. supported_by: - reference_id: PMID:30021884 supporting_text: >- Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:33961781 qualifier: enables review: 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. action: MARK_AS_OVER_ANNOTATED 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. supported_by: - reference_id: PMID:33961781 supporting_text: >- Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. - term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in review: summary: >- Automated electronic annotation of ER localization, redundant with but consistent with the experimental IDA and IBA ER annotations for this gene. action: ACCEPT reason: >- Correct ER location, the validated functional compartment; consistent with the experimental IDA evidence for this gene. supported_by: - reference_id: PMID:19846465 supporting_text: >- CRTAP and P3H1 form a complex with cyclophilin B (CyPB) in the endoplasmic reticulum (ER) - term: id: GO:0007283 label: spermatogenesis evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in review: 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. action: MARK_AS_OVER_ANNOTATED reason: >- Broad ortholog-transfer annotation lacking human evidence and unrelated to the validated collagen-modification/chaperone function of CRTAP. supported_by: - reference_id: GO_REF:0000107 supporting_text: >- Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:39245686 qualifier: enables review: 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. action: MARK_AS_OVER_ANNOTATED 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. supported_by: - reference_id: PMID:39245686 supporting_text: >- We determine cryo-EM structures of the P3H1/CRTAP/PPIB complex. - term: id: GO:0050821 label: protein stabilization evidence_type: IMP original_reference_id: PMID:19846465 qualifier: involved_in review: 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). action: ACCEPT reason: >- Directly demonstrated by IMP in patient fibroblasts; CRTAP stabilizes its complex partner P3H1, a core aspect of complex assembly and integrity. supported_by: - reference_id: PMID:19846465 supporting_text: >- These data indicate that CRTAP and P3H1 are mutually stabilized in the collagen prolyl 3-hydroxylation complex. - term: id: GO:0006457 label: protein folding evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: involved_in review: 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. action: MODIFY reason: >- Supported chaperone/foldase activity, but the generic protein folding term can be made more precise to reflect the ER collagen-folding role. proposed_replacement_terms: - id: GO:0034975 label: protein folding in endoplasmic reticulum supported_by: - reference_id: PMID:20089953 supporting_text: >- 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. - term: id: GO:0032991 label: protein-containing complex evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: part_of review: 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. action: KEEP_AS_NON_CORE reason: >- Correct but generic; complex membership in the specific prolyl 3-hydroxylation complex is captured in core_functions (in_complex). supported_by: - reference_id: PMID:39245686 supporting_text: >- We determine cryo-EM structures of the P3H1/CRTAP/PPIB complex. - term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IDA original_reference_id: PMID:20089953 qualifier: located_in review: summary: >- Direct immunofluorescence localization of endogenous CRTAP to the ER in human fibroblasts. This is strong, primary evidence for the core ER location. action: ACCEPT reason: >- Direct experimental localization to the ER, the validated functional compartment for CRTAP. supported_by: - reference_id: PMID:20089953 supporting_text: >- 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. - term: id: GO:0005576 label: extracellular region evidence_type: IDA original_reference_id: PMID:19846465 qualifier: located_in review: 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. action: KEEP_AS_NON_CORE reason: >- Experimentally observed secreted pool, but a minor fraction relative to the ER-resident function; not a core localization. supported_by: - reference_id: PMID:19846465 supporting_text: >- in conditioned media from control cells ... about 10-12% of total CRTAP is secreted - term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IDA original_reference_id: PMID:19846465 qualifier: located_in review: 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. action: ACCEPT reason: >- Direct experimental evidence for the core ER location of CRTAP. supported_by: - reference_id: PMID:19846465 supporting_text: >- CRTAP and P3H1 form a complex with cyclophilin B (CyPB) in the endoplasmic reticulum (ER) - term: id: GO:1901874 label: negative regulation of post-translational protein modification evidence_type: IMP original_reference_id: PMID:19846465 qualifier: involved_in review: 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. action: KEEP_AS_NON_CORE reason: >- Supported as an indirect/consequential phenotype of delayed-folding prevention; not a direct molecular regulatory function of CRTAP. supported_by: - reference_id: PMID:19846465 supporting_text: >- Excess modification, or 'overmodification' of the collagen helix can be detected as delayed electrophoretic migration of collagen alpha chains - term: id: GO:0005788 label: endoplasmic reticulum lumen evidence_type: TAS original_reference_id: Reactome:R-HSA-1980233 qualifier: located_in review: 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. action: ACCEPT reason: >- Accurate and more precise than endoplasmic reticulum; the ER lumen is the validated site of complex activity. supported_by: - reference_id: PMID:19846465 supporting_text: >- CRTAP and P3H1 form a complex with cyclophilin B (CyPB) in the endoplasmic reticulum (ER) which 3-hydroxylates the Pro986 residue - term: id: GO:0005788 label: endoplasmic reticulum lumen evidence_type: TAS original_reference_id: Reactome:R-HSA-2022073 qualifier: located_in review: summary: >- Redundant Reactome ER-lumen localization (procollagen triple helix formation reaction). Correct and consistent with the validated ER-luminal location. action: ACCEPT reason: >- Correct, precise ER-lumen location consistent with the accepted ER-lumen annotation; retained as a redundant but valid localization. supported_by: - reference_id: PMID:39245686 supporting_text: >- the modifications of proline residues play critical roles in the formation of triple helix and the maintenance of stability - term: id: GO:0005788 label: endoplasmic reticulum lumen evidence_type: TAS original_reference_id: Reactome:R-HSA-8948226 qualifier: located_in review: summary: >- Redundant Reactome ER-lumen localization (prolyl 3-hydroxylase complex dissociation reaction). Correct location, consistent with the accepted ER-lumen annotation. action: ACCEPT reason: >- Correct, precise ER-lumen location consistent with the accepted ER-lumen annotation; retained as a redundant but valid localization. supported_by: - reference_id: PMID:19846465 supporting_text: >- the collagen prolyl 3-hydroxylation complex in the endoplasmic reticulum (ER) - term: id: GO:0005788 label: endoplasmic reticulum lumen evidence_type: TAS original_reference_id: Reactome:R-HSA-8948230 qualifier: located_in review: summary: >- Redundant Reactome ER-lumen localization (P3HB binds 4-Hyp-collagen propeptides reaction). Correct location, consistent with the accepted ER-lumen annotation. action: ACCEPT reason: >- Correct, precise ER-lumen location consistent with the accepted ER-lumen annotation; retained as a redundant but valid localization. supported_by: - reference_id: PMID:19846465 supporting_text: >- the collagen prolyl 3-hydroxylation complex in the endoplasmic reticulum (ER) references: - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000107 title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:17055431 title: CRTAP is required for prolyl 3-hydroxylation and mutations cause recessive osteogenesis imperfecta. findings: - statement: >- CRTAP is required for efficient 3-hydroxylation of fibrillar collagen prolyl residues; loss-of-function mutations cause recessive osteogenesis imperfecta. reference_section_type: ABSTRACT - id: PMID:19846465 title: Prolyl 3-hydroxylase 1 and CRTAP are mutually stabilizing in the endoplasmic reticulum collagen prolyl 3-hydroxylation complex. findings: - statement: >- CRTAP, P3H1 and cyclophilin B form the ER collagen prolyl 3-hydroxylation complex that 3-hydroxylates Pro986 of alpha1(I)/alpha1(II) chains; CRTAP and P3H1 are mutually stabilized, and the complex also acts as a chaperone. reference_section_type: ABSTRACT - id: PMID:20089953 title: Lack of cyclophilin B in osteogenesis imperfecta with normal collagen folding. findings: - statement: >- Confirms CRTAP as a component of the P3H1/CRTAP/CyPB complex; absence of P3H1 or CRTAP decreases Pro986 3-hydroxylation and delays collagen folding. reference_section_type: ABSTRACT - id: PMID:30021884 title: Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. findings: [] - id: PMID:33961781 title: Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. findings: [] - id: PMID:39245686 title: The structural basis for the collagen processing by human P3H1/CRTAP/PPIB ternary complex. findings: - statement: >- Cryo-EM structures of the human P3H1/CRTAP/PPIB ternary complex; P3H1 and PPIB active sites form a bifunctional reaction center and CRTAP contributes to a multi-site collagen substrate-interacting zone. reference_section_type: ABSTRACT - id: Reactome:R-HSA-1980233 title: Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen findings: [] - id: Reactome:R-HSA-2022073 title: Procollagen triple helix formation findings: [] - id: Reactome:R-HSA-8948226 title: Prolyl 3-hydroxylases:Fe2+:3,4-Hyp collagen propeptides dissociates findings: [] - id: Reactome:R-HSA-8948230 title: P3HB binds 4-Hyp-collagen propeptides findings: [] core_functions: - description: >- Non-catalytic scaffolding/helper subunit of the ER collagen prolyl 3-hydroxylation complex (with P3H1 and PPIB). CRTAP is required for assembly, stability and activity of the complex that 3-hydroxylates Pro986 of alpha1(I) and alpha1(II) fibrillar procollagen chains; CRTAP contributes to collagen substrate binding but does not itself catalyze hydroxylation. supported_by: - reference_id: PMID:19846465 supporting_text: >- 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. - reference_id: PMID:39245686 supporting_text: >- The structure of the P3H1/CRTAP/PPIB/collagen peptide complex reveals multiple binding sites, suggesting a substrate interacting zone. molecular_function: id: GO:0005198 label: structural molecule activity contributes_to_molecular_function: id: GO:0005518 label: collagen binding directly_involved_in: - id: GO:0032964 label: collagen biosynthetic process locations: - id: GO:0005788 label: endoplasmic reticulum lumen substrates: - id: GO:0005518 label: collagen binding in_complex: id: GO:0032991 label: protein-containing complex - description: >- Collagen-specific molecular chaperone/foldase activity of the complex: CRTAP is required for normal collagen triple-helix folding rate, and its loss causes delayed folding and overmodification of the collagen helix. CRTAP also mutually stabilizes its complex partner P3H1 in the ER. supported_by: - reference_id: PMID:20089953 supporting_text: >- 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. - reference_id: PMID:19846465 supporting_text: >- These data indicate that CRTAP and P3H1 are mutually stabilized in the collagen prolyl 3-hydroxylation complex. molecular_function: id: GO:0044183 label: protein folding chaperone directly_involved_in: - id: GO:0034975 label: protein folding in endoplasmic reticulum - id: GO:0050821 label: protein stabilization locations: - id: GO:0005788 label: endoplasmic reticulum lumen proposed_new_terms: [] suggested_questions: - question: >- 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? - question: >- 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? suggested_experiments: - description: >- 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. - description: >- 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. - description: >- 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.