id: Q6UX04 gene_symbol: CWC27 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- CWC27 (also known as NY-CO-10 and SDCCAG10) is a nuclear, spliceosome-associated protein of the cyclophilin-type peptidyl-prolyl isomerase (PPIase) family. It has an N-terminal cyclophilin-like domain followed by a long disordered, partly coiled-coil C-terminal region. Although it belongs to the cyclophilin family, the CWC27 cyclophilin domain is a degenerate (catalytically inactive) pseudo-enzyme: it carries a glutamate in place of a conserved active-site residue and shows no detectable peptidyl-prolyl cis-trans isomerase activity and no cyclosporin binding. Functionally, CWC27 is a structural/scaffold component of the spliceosome. It is recruited during spliceosome activation as part of the activated Bact complex of the major (U2-type) spliceosome and is among the first factors released during the Bact-to-B* transition; it is also a component of the activated minor (U12-type) spliceosome, contributing to splicing of U12-type introns. In the major spliceosome the endonuclease-like domain of PRP8 contacts CWC27, and CWC27 works with its partner CWC22 in pre-mRNA splicing and exon junction complex deposition. Biallelic loss-of-function variants in CWC27 cause autosomal-recessive retinitis pigmentosa with or without skeletal and other developmental anomalies (RPSKA), underscoring its essential role in pre-mRNA splicing. alternative_products: - name: '1' id: Q6UX04-1 - name: '2' id: Q6UX04-2 sequence_note: VSP_030082, VSP_030083 existing_annotations: - term: id: GO:0071013 label: catalytic step 2 spliceosome evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: part_of review: summary: >- Phylogenetic (IBA) inference that CWC27 is part of the catalytic step 2 spliceosome, transferred across the Cwc27 ortholog tree. CWC27 is genuinely a spliceosome component, but cryo-EM evidence places it specifically in the activated Bact (U2-type precatalytic-to-activated) stage, from which it is released before the step 2 (C*) reaction. action: KEEP_AS_NON_CORE reason: >- CWC27 is correctly a spliceosomal component, so the broad family-level placement in a catalytic spliceosome is not wrong. However, structural studies show CWC27/NY-CO-10 is recruited to the activated Bact complex and released during the Bact-to-B* transition, so it is not specifically a step 2 catalytic spliceosome factor. Retained as a non-core membership term; the more precise activated-spliceosome terms (GO:0071005, GO:0005681) better capture its role. supported_by: - reference_id: PMID:29360106 supporting_text: >- the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in review: summary: >- Automated (IEA) annotation of nuclear localization, consistent with CWC27's role as a spliceosomal protein and with UniProt's curated subcellular location (Nucleus). action: ACCEPT reason: >- Nuclear localization is well supported. UniProt records the subcellular location as Nucleus, and CWC27 is a component of nuclear spliceosomal complexes. More specific nucleoplasm annotations (GO:0005654) are also present. supported_by: - reference_id: file:human/CWC27/CWC27-uniprot.txt supporting_text: "SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}." - term: id: GO:0006457 label: protein folding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: summary: >- InterPro2GO (IEA) transfer of protein folding based solely on the cyclophilin-type PPIase InterPro signature (IPR020892). This is a family-level inference that assumes foldase/chaperone activity from domain membership. action: MARK_AS_OVER_ANNOTATED reason: >- CWC27 is a demonstrated catalytically inactive pseudo-PPIase: it shows no peptidyl-prolyl cis-trans isomerase activity and no cyclosporin binding, and UniProt curates it as a "Probable inactive peptidyl-prolyl cis-trans isomerase" with a CAUTION. The InterPro2GO "protein folding" transfer ignores the loss of catalytic residues and therefore over-annotates a foldase/chaperone function that CWC27 does not possess. There is no evidence CWC27 catalyzes or assists protein folding. supported_by: - reference_id: PMID:20676357 supporting_text: >- No binding was detected for PPIL2, PPIL6, or SDCCAG-10, making these, to our knowledge, the first set of human cyclophilins that have been found incompetent to ligate cyclosporin - reference_id: file:human/CWC27/CWC27-uniprot.txt supporting_text: >- Despite the fact that it belongs to the cyclophilin-type PPIase family, a report has shown that it has probably no peptidyl-prolyl cis-trans isomerase activity. - reference_id: file:human/CWC27/CWC27-deep-research-falcon.md supporting_text: >- This loss of catalytic function is directly attributable to the Glu122 substitution in the active site, which renders the enzyme incompetent for proline isomerization - term: id: GO:0000398 label: mRNA splicing, via spliceosome evidence_type: NAS original_reference_id: PMID:29360106 qualifier: involved_in review: summary: >- NAS annotation (ComplexPortal) that CWC27 functions in pre-mRNA splicing via the spliceosome, based on its presence in the activated major spliceosome. action: ACCEPT reason: >- mRNA splicing via the spliceosome is the core biological process of CWC27. CWC27/NY-CO-10 is a component of the activated (Bact) major spliceosome resolved by cryo-EM, and biallelic loss of function causes a Mendelian disease consistent with impaired splicing. As a non-catalytic scaffold, CWC27 also forms a heterodimer with CWC22 that the falcon deep research describes as a landing platform coupling spliceosome activation to eIF4A3/exon junction complex recruitment, consistent with its splicing role. supported_by: - reference_id: PMID:29360106 supporting_text: >- the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) - reference_id: file:human/CWC27/CWC27-deep-research-falcon.md supporting_text: >- A critical function of CWC27 is its formation of a heterodimer with CWC22, another spliceosomal protein - term: id: GO:0000398 label: mRNA splicing, via spliceosome evidence_type: NAS original_reference_id: PMID:33509932 qualifier: involved_in review: summary: >- NAS annotation (ComplexPortal) that CWC27 functions in pre-mRNA splicing, based on its presence in the activated human minor (U12-type) spliceosome. action: ACCEPT reason: >- CWC27 is a component of the activated minor spliceosome that splices U12-type introns, directly supporting its involvement in mRNA splicing via the spliceosome. supported_by: - reference_id: PMID:33509932 supporting_text: The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. - term: id: GO:0005681 label: spliceosomal complex evidence_type: IPI original_reference_id: PMID:39068178 qualifier: part_of review: summary: >- IPI annotation (ComplexPortal) placing CWC27 as part of the spliceosomal complex, based on identification within activation-stage spliceosome structures. action: ACCEPT reason: >- Spliceosome membership is directly and unambiguously supported by cryo-EM structures of the human spliceosome capturing the activation pathway (pre-Bact through post-Bact). This is a core cellular-component annotation for CWC27. supported_by: - reference_id: PMID:39068178 supporting_text: >- intermediate states between the B and B* complexes: pre-Bact, Bact-I, Bact-II, Bact-III, Bact-IV, and post-Bact - term: id: GO:0071018 label: U12-type catalytic step 2 spliceosome evidence_type: IPI original_reference_id: PMID:33509932 qualifier: part_of review: summary: >- IPI annotation placing CWC27 as part of the U12-type (minor) catalytic step 2 spliceosome, based on the cryo-EM structure of the activated human minor spliceosome. action: KEEP_AS_NON_CORE reason: >- CWC27 is a genuine component of the activated minor spliceosome, so minor (U12-type) spliceosome membership is correct. Retained as non-core: as in the major spliceosome, CWC27 associates with the activated complex and the precise catalytic-step-2 placement is a curated mapping of the resolved minor spliceosome state rather than evidence of a step 2 catalytic role for CWC27. supported_by: - reference_id: PMID:33509932 supporting_text: >- Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. - term: id: GO:0005654 label: nucleoplasm evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: >- IDA annotation (HPA immunofluorescence) localizing CWC27 to the nucleoplasm. action: ACCEPT reason: >- Nucleoplasmic localization is consistent with CWC27's role as a spliceosomal protein and with the curated UniProt nuclear localization. Direct immunofluorescence evidence supports this subcellular component. supported_by: - reference_id: file:human/CWC27/CWC27-uniprot.txt supporting_text: "SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}." - term: id: GO:0000398 label: mRNA splicing, via spliceosome evidence_type: IC original_reference_id: PMID:29360106 qualifier: involved_in review: summary: >- IC annotation inferring involvement in mRNA splicing from membership in the U2-type precatalytic/activated spliceosome (GO:0071005). action: ACCEPT reason: >- A sound curator inference: CWC27 is a structural component of the activated major spliceosome, so it is reasonably inferred to be involved in mRNA splicing via the spliceosome, the core process for this protein. supported_by: - reference_id: PMID:29360106 supporting_text: >- the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) - term: id: GO:0071005 label: U2-type precatalytic spliceosome evidence_type: IDA original_reference_id: PMID:29360106 qualifier: part_of review: summary: >- IDA annotation placing CWC27 in the U2-type (major) precatalytic/activated spliceosome, based on the cryo-EM structure of the human activated spliceosome. action: ACCEPT reason: >- This is the most precisely evidenced cellular-component annotation for CWC27. Cryo-EM directly visualizes NY-CO-10 (CWC27) in the activated major (Bact) spliceosome, with the PRP8 endonuclease-like domain contacting it, and shows it is released during the Bact-to-B* transition. The falcon deep research adds the mechanistic detail that release is driven by the DEAH-box helicase PRP2 (with SPP2), which during the Bact-to-B* transition triggers dissociation of CWC27 along with the SF3a/SF3b and RES complexes. supported_by: - reference_id: PMID:29360106 supporting_text: >- the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) - reference_id: file:human/CWC27/CWC27-deep-research-falcon.md supporting_text: >- The DEAH-box helicase PRP2, assisted by its co-activator SPP2, pulls on the 3' end of the intron, leading to dissociation of the SF3a/SF3b complexes, RES complex, and importantly, both CWC24 and CWC27 - term: id: GO:0003755 label: peptidyl-prolyl cis-trans isomerase activity evidence_type: IDA original_reference_id: PMID:20676357 qualifier: enables negated: true review: summary: >- Negated (NOT) IDA annotation recording that CWC27 (SDCCAG-10) does NOT have peptidyl-prolyl cis-trans isomerase activity, based on direct biochemical assay showing no tetrapeptide isomerase activity and no cyclosporin binding. action: ACCEPT reason: >- This negated annotation correctly captures the experimental finding that CWC27 is a catalytically inactive pseudo-PPIase. Davis et al. found SDCCAG-10 (CWC27) incompetent for both cyclosporin binding and tetrapeptide isomerase activity, attributable to a glutamate substitution at a conserved active-site position. The NOT annotation should be retained as it documents the absence of the family-expected catalytic activity. supported_by: - reference_id: PMID:20676357 supporting_text: >- No binding was detected for PPIL2, PPIL6, or SDCCAG-10, making these, to our knowledge, the first set of human cyclophilins that have been found incompetent to ligate cyclosporin - term: id: GO:0005654 label: nucleoplasm evidence_type: TAS original_reference_id: Reactome:R-HSA-9770131 qualifier: located_in review: summary: >- TAS annotation (Reactome, Formation of the Spliceosomal B* complex) localizing CWC27 to the nucleoplasm. action: ACCEPT reason: >- Nucleoplasmic localization is consistent with CWC27's spliceosomal function and with the curated UniProt nuclear localization and HPA immunofluorescence evidence. supported_by: - reference_id: file:human/CWC27/CWC27-uniprot.txt supporting_text: "SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}." - term: id: GO:0005654 label: nucleoplasm evidence_type: TAS original_reference_id: Reactome:R-HSA-9770145 qualifier: located_in review: summary: >- TAS annotation (Reactome, Formation of the Spliceosomal Bact complex) localizing CWC27 to the nucleoplasm. action: ACCEPT reason: >- Consistent with CWC27's recruitment into the activated Bact spliceosome in the nucleoplasm; supported by curated nuclear localization and immunofluorescence. supported_by: - reference_id: file:human/CWC27/CWC27-uniprot.txt supporting_text: "SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}." - term: id: GO:0005654 label: nucleoplasm evidence_type: TAS original_reference_id: Reactome:R-HSA-9921507 qualifier: located_in review: summary: >- TAS annotation (Reactome, NS5 interacts with Spliceosome) localizing CWC27 to the nucleoplasm. action: ACCEPT reason: >- Nucleoplasmic localization is well supported for this spliceosomal protein. The annotation derives from a Reactome pathway in which the spliceosome (with CWC27) resides in the nucleoplasm. supported_by: - reference_id: file:human/CWC27/CWC27-uniprot.txt supporting_text: "SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}." - term: id: GO:0000398 label: mRNA splicing, via spliceosome evidence_type: IC original_reference_id: PMID:11991638 qualifier: involved_in review: summary: >- IC annotation inferring involvement in mRNA splicing from CWC27's presence in native purified spliceosomes (catalytic step 2 / C-complex-enriched). action: ACCEPT reason: >- CWC27 is detected in native purified spliceosomes, supporting the inference that it participates in mRNA splicing via the spliceosome, its core process. supported_by: - reference_id: PMID:11991638 supporting_text: >- These spliceosomes consist largely of C complex containing splicing - term: id: GO:0071013 label: catalytic step 2 spliceosome evidence_type: IDA original_reference_id: PMID:11991638 qualifier: part_of review: summary: >- IDA annotation placing CWC27 in the catalytic step 2 spliceosome, based on its identification in native purified C-complex-enriched spliceosomes. action: KEEP_AS_NON_CORE reason: >- CWC27 was detected in native purified spliceosome preparations enriched for C complex, supporting spliceosome membership. However, higher-resolution cryo-EM work later localized CWC27/NY-CO-10 specifically to the activated Bact stage, from which it is released before step 2 catalysis. The catalytic step 2 placement reflects the bulk composition of the purified preparation rather than a specific step 2 role, so it is retained as a non-core membership term. supported_by: - reference_id: PMID:11991638 supporting_text: >- These spliceosomes consist largely of C complex containing splicing - reference_id: PMID:29360106 supporting_text: >- the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) core_functions: - description: >- Structural/scaffold component of the activated spliceosome required for pre-mRNA splicing; CWC27 is recruited to the activated Bact complex of the major (U2-type) spliceosome and is released during the Bact-to-B* transition, and is likewise a component of the activated minor (U12-type) spliceosome. supported_by: - reference_id: PMID:29360106 supporting_text: >- the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) - reference_id: PMID:33509932 supporting_text: The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. - reference_id: file:human/CWC27/CWC27-deep-research-falcon.md supporting_text: >- A critical function of CWC27 is its formation of a heterodimer with CWC22, another spliceosomal protein directly_involved_in: - id: GO:0000398 label: mRNA splicing, via spliceosome in_complex: id: GO:0005681 label: spliceosomal complex locations: - id: GO:0005654 label: nucleoplasm proposed_new_terms: [] suggested_questions: - question: Does the catalytically dead cyclophilin domain of CWC27 retain a substrate-binding or proline-recognition function within the spliceosome that contributes to splice site fidelity, even in the absence of isomerase catalysis? - question: How does the CWC27-CWC22 module mechanistically couple spliceosome activation to positioning of eIF4A3/the exon junction complex, and which step of EJC deposition requires CWC27? - question: Why do CWC27 loss-of-function variants produce a retina-predominant phenotype (RPSKA) despite ubiquitous expression and an essential splicing role? suggested_experiments: - description: Structure-guided mutagenesis of the degenerate active-site residue(s) (e.g., the Glu at the position equivalent to PPIA Trp121) combined with rescue assays in CWC27-null cells to test whether restoring a canonical cyclophilin active site confers PPIase activity and/or alters splicing. - description: Transcriptome-wide splicing analysis (RNA-seq/junction analysis) in CWC27-depleted cells, with emphasis on U12-type minor introns and retina-expressed transcripts, to define the set of introns dependent on CWC27. - description: Cross-linking/proteomics and cryo-EM of the CWC27-CWC22 sub-complex bound to eIF4A3 to map the interface and test the model that CWC27 positions the EJC core for deposition during splicing. 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:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:11991638 title: Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. findings: - statement: >- CWC27 is present in native affinity-purified spliceosomes consisting largely of C complex, the basis for its catalytic step 2 spliceosome annotation. - id: PMID:20676357 title: Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. findings: - statement: >- CWC27 (SDCCAG-10) is a catalytically inactive cyclophilin with no detectable cyclosporin binding and no tetrapeptide isomerase activity. - id: PMID:29360106 title: Structure of the human activated spliceosome in three conformational states. findings: - statement: >- CWC27/NY-CO-10 is a component of the activated major (Bact) spliceosome and is released during the Bact-to-B* transition. - id: PMID:33509932 title: Structure of the activated human minor spliceosome. findings: - statement: >- CWC27 is a component of the activated human minor spliceosome that splices U12-type introns. - id: PMID:39068178 title: Molecular basis for the activation of human spliceosome. findings: - statement: >- CWC27 is identified within spliceosome activation intermediates spanning the pre-Bact to post-Bact states. - id: PMID:28285769 title: Mutations in the spliceosome component CWC27 cause retinal degeneration with or without additional developmental anomalies. findings: - statement: >- Biallelic loss-of-function variants in CWC27 cause autosomal-recessive retinitis pigmentosa with or without skeletal/developmental anomalies (RPSKA). - id: Reactome:R-HSA-9770131 title: Formation of the Spliceosomal B* complex findings: [] - id: Reactome:R-HSA-9770145 title: Formation of the Spliceosomal Bact complex findings: [] - id: Reactome:R-HSA-9921507 title: NS5 interacts with Spliceosome findings: [] - id: file:human/CWC27/CWC27-deep-research-falcon.md title: Falcon deep research report for CWC27 findings: - statement: >- Synthesizes CWC27 as a catalytically inactive spliceosomal cyclophilin that acts as a structural/scaffold splicing factor; recruited to the activated Bact complex, released by the PRP2 helicase during the Bact-to-B* transition, and forming a CWC27-CWC22 heterodimer that serves as a landing platform for eIF4A3/EJC recruitment. reference_review: relevance: HIGH correctness: UNVERIFIED review_notes: >- LLM-synthesized deep research; consistent with the curated picture (degenerate PPIase, Bact-stage structural splicing factor, CWC27-CWC22/EJC role, retinal spliceosomopathy) and correctly states CWC27 is catalytically inactive as a PPIase (Glu122 substitution, no cyclosporin binding). Its underlying primary citations (Bertrand 2022, Schlautmann 2020, Rajiv 2018, Schmitzova 2023, Zhan 2024) were not independently verified here and are not in the publication cache, so correctness left UNVERIFIED. Note the report does NOT overstate active isomerase catalysis; quoted passages were checked verbatim.