{"gene":"CCDC47","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2020,"finding":"CCDC47 is a component of a ~360 kDa ribosome-associated ER translocon complex (alongside Sec61, TMCO1, Nicalin, TMEM147, and NOMO) that selectively engages hundreds of multi-pass membrane protein clients; cryo-EM reveals CCDC47 as part of a large assembly at the ribosome exit tunnel organized around a central membrane cavity, and cells lacking CCDC47 show reduced levels of the multi-pass client EAAT1.","method":"Cryo-electron microscopy, high-throughput mRNA sequencing, cell-based loss-of-function (accessory component knockout)","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure plus functional client-protein assay, replicated by independent lab (PMID:32814900) in the same year","pmids":["32820719"],"is_preprint":false},{"year":2020,"finding":"CCDC47 forms an obligate heterodimeric intramembrane chaperone complex (the PAT complex) with Asterix (WDR83OS product). The PAT complex engages nascent transmembrane domains containing unshielded hydrophilic side chains within the lipid bilayer and disengages upon substrate folding; cells lacking either subunit show reduced biogenesis of numerous multi-spanning membrane proteins.","method":"Co-immunoprecipitation, reconstitution of PAT complex, loss-of-function cell assays measuring multi-spanning membrane protein levels","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP establishing obligate heterodimer, functional KO phenotype across numerous substrates, independently replicated structurally (PMID:36261528)","pmids":["32814900"],"is_preprint":false},{"year":2022,"finding":"Structural and biochemical analysis of multipass protein biogenesis intermediates showed that CCDC47 occludes and latches the Sec61 lateral gate closed, preventing nascent chain engagement with Sec61; instead, Asterix binds and redirects the substrate to a position behind Sec61 within a semi-enclosed, lipid-filled cavity formed by the PAT complex and multipass translocon. Multiple TMDs are detected in this cavity after emerging from the ribosome, indicating that multipass proteins insert and fold behind Sec61.","method":"Cryo-electron microscopy, biochemical trapping of biogenesis intermediates, Sec61 lateral gate inhibitor assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure of biogenesis intermediates combined with biochemical and pharmacological orthogonal methods in a single rigorous study","pmids":["36261528"],"is_preprint":false},{"year":2014,"finding":"Calumin (CCDC47) co-immunoprecipitates with ERAD components p97, BIP, Derlin-1, Derlin-2, and VIMP, and its knockdown in HEK293 cells reduces ERAD efficiency, as shown by attenuated degradation of misfolded α1-antitrypsin and impaired ER-to-cytosol dislocation of cholera toxin A1 subunit; loss of calumin in mouse embryos causes ER stress-associated alterations in yolk sac endoderm, contributing to embryonic lethality.","method":"Co-immunoprecipitation, siRNA knockdown with ERAD functional assays (misfolded protein degradation, cholera toxin dislocation), mouse knockout embryo analysis","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with multiple ERAD partners plus two orthogonal functional ERAD assays in a single study","pmids":["25009997"],"is_preprint":false},{"year":2018,"finding":"Bi-allelic loss-of-function variants in CCDC47 cause reduced total ER Ca2+ storage, impaired IP3R-mediated Ca2+ release, and reduced ER Ca2+ refilling via store-operated Ca2+ entry (SOCE) in patient-derived cells, establishing CCDC47 as required for ER Ca2+ homeostasis.","method":"Patient cell characterization, Ca2+ signaling assays (ER Ca2+ store measurement, IP3R release assay, SOCE measurement), mRNA/protein quantification","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal Ca2+ assays in patient-derived cells, single lab","pmids":["30401460"],"is_preprint":false},{"year":2018,"finding":"Overexpression of CCDC47 in rat H9C2 cardiomyocytes increases ionomycin-induced Ca2+ release and reuptake, demonstrating a positive role for CCDC47 in ER/SR Ca2+ handling in cardiomyocytes.","method":"Overexpression in rat cardiomyocyte cell line, ionomycin-induced Ca2+ release/reuptake assay","journal":"Cell & bioscience","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single overexpression experiment in a cell line, single lab, single method","pmids":["30140426"],"is_preprint":false},{"year":2025,"finding":"In a fungal (Chaetomium thermophilum) SND3 translocon cryo-EM structure, CCDC47 is present alongside SEC61 and TRAPα; the SEC61β N-terminus works together with CCDC47 to prevent substrate access to the SEC61 translocon within this SND pathway complex.","method":"Cryo-electron microscopy of ribosome-associated SND3 translocon complex","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — cryo-EM structure establishes CCDC47 position and role in gating, but single study in a fungal ortholog context","pmids":["41162385"],"is_preprint":false},{"year":2025,"finding":"CCDC47 co-immunoprecipitates with pancreas-specific SPCA2C (Atp2c2c) and with STIM1 and Orai1; co-expression of CCDC47 and SPCA2C increases store-operated Ca2+ entry (SOCE) and resting cytosolic Ca2+ above either protein alone. These interactions depend on the CCDC47 coiled-coil domain or accessible transmembrane domains.","method":"Co-immunoprecipitation, co-localization microscopy, co-expression functional SOCE assay in HEK-Orai1YFP cells, domain-deletion experiments","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and functional co-expression assay with domain-deletion mapping, single lab","pmids":["40783819"],"is_preprint":false}],"current_model":"CCDC47 is an ER-resident transmembrane protein that functions primarily as the obligate partner of Asterix in the PAT intramembrane chaperone complex, which occludes the Sec61 lateral gate and redirects nascent hydrophilic transmembrane domains to a lipid-filled cavity behind Sec61 for co-translational folding of multi-pass membrane proteins; it additionally participates in ERAD through interactions with p97, BIP, and Derlin family proteins, and contributes to ER Ca2+ homeostasis by supporting IP3R-mediated Ca2+ release and store-operated Ca2+ entry."},"narrative":{"mechanistic_narrative":"CCDC47 is an ER-resident component of the ribosome-associated multipass translocon that governs the co-translational biogenesis of multi-spanning membrane proteins [PMID:32820719]. It functions as the obligate heterodimeric partner of Asterix (WDR83OS) in the PAT intramembrane chaperone complex, which engages nascent transmembrane domains bearing unshielded hydrophilic side chains within the bilayer and disengages once the substrate folds; loss of either subunit reduces the biogenesis of numerous multi-spanning membrane proteins [PMID:32814900]. Mechanistically, CCDC47 occludes and latches the Sec61 lateral gate closed, while Asterix captures the substrate and redirects it to a semi-enclosed, lipid-filled cavity behind Sec61 where multiple TMDs insert and fold [PMID:36261528]; a gating role for CCDC47 in restricting Sec61 access is structurally conserved in a fungal SND translocon [PMID:41162385]. Independently of this chaperone role, CCDC47 participates in ER-associated degradation, co-immunoprecipitating with p97, BIP, Derlin-1, Derlin-2, and VIMP and supporting misfolded-protein turnover and ER-to-cytosol dislocation [PMID:25009997], and it is required for ER Ca2+ homeostasis, with bi-allelic loss-of-function variants in patients impairing ER Ca2+ storage, IP3R-mediated release, and store-operated Ca2+ entry [PMID:30401460]. Loss of CCDC47 in mouse embryos causes ER stress and embryonic lethality [PMID:25009997].","teleology":[{"year":2014,"claim":"Established the first molecular role for CCDC47 (calumin) by placing it in the ERAD machinery, addressing what cellular process this ER protein serves.","evidence":"Co-IP with p97/BIP/Derlin-1/Derlin-2/VIMP plus ERAD functional assays and knockout mouse embryo analysis","pmids":["25009997"],"confidence":"High","gaps":["Did not resolve whether CCDC47 acts directly in dislocation or as a scaffold","No structural basis for the ERAD partner interactions","Relationship to its later-defined chaperone role left undefined"]},{"year":2018,"claim":"Linked CCDC47 to ER Ca2+ homeostasis in humans, showing its loss disrupts Ca2+ storage and signaling and answering whether CCDC47 dysfunction has a physiological/clinical consequence.","evidence":"Patient-derived cells with bi-allelic loss-of-function variants assayed for ER Ca2+ stores, IP3R release, and SOCE","pmids":["30401460"],"confidence":"Medium","gaps":["Mechanism connecting CCDC47 to IP3R and SOCE machinery not defined","Single lab","Whether Ca2+ defects are direct or secondary to translocon/ERAD dysfunction unresolved"]},{"year":2018,"claim":"Provided a gain-of-function correlate for the Ca2+ role, showing CCDC47 overexpression enhances cardiomyocyte Ca2+ release and reuptake.","evidence":"CCDC47 overexpression in rat H9C2 cells with ionomycin-induced Ca2+ assay","pmids":["30140426"],"confidence":"Low","gaps":["Single overexpression experiment in one cell line and method","No mechanistic interaction established","Not validated by loss-of-function"]},{"year":2020,"claim":"Defined CCDC47 as a constituent of a large ribosome-associated multipass translocon selective for multi-spanning clients, reframing it as a biogenesis factor.","evidence":"Cryo-EM of the ~360 kDa translocon, client mRNA-seq profiling, and knockout reducing the multi-pass client EAAT1","pmids":["32820719"],"confidence":"High","gaps":["Did not define CCDC47's specific molecular action within the assembly","Mechanism of client selectivity unresolved"]},{"year":2020,"claim":"Identified the obligate CCDC47–Asterix PAT heterodimer as an intramembrane chaperone that engages unshielded TMDs, establishing the molecular function underlying multipass biogenesis.","evidence":"Reciprocal Co-IP, PAT complex reconstitution, and loss-of-function assays across many multi-spanning substrates","pmids":["32814900"],"confidence":"High","gaps":["Did not yet show the structural mechanism of substrate handoff","Division of labor between CCDC47 and Asterix not resolved at this stage"]},{"year":2022,"claim":"Resolved the mechanism of action: CCDC47 latches the Sec61 lateral gate closed while Asterix redirects substrates into a lipid-filled cavity behind Sec61 for folding.","evidence":"Cryo-EM of trapped biogenesis intermediates with biochemical trapping and Sec61 lateral-gate inhibitor assays","pmids":["36261528"],"confidence":"High","gaps":["Dynamics and kinetics of gate latching not quantified","How specific TMD features trigger PAT engagement/release not fully defined"]},{"year":2025,"claim":"Showed CCDC47-mediated gating of the Sec61 translocon is conserved in a fungal SND-pathway translocon, generalizing the latching role.","evidence":"Cryo-EM of the Chaetomium thermophilum SND3 translocon with SEC61 and TRAPα","pmids":["41162385"],"confidence":"Medium","gaps":["Single study in a fungal ortholog","Functional consequence of SND-context gating not assayed"]},{"year":2025,"claim":"Connected CCDC47 physically to SOCE machinery, identifying SPCA2C, STIM1, and Orai1 partners and a domain dependence for Ca2+ enhancement.","evidence":"Co-IP, co-localization, co-expression SOCE assays in HEK-Orai1 cells, and domain-deletion mapping to the coiled-coil/TM regions","pmids":["40783819"],"confidence":"Medium","gaps":["Single lab","Whether interactions are direct vs. complex-mediated not established","Physiological relevance beyond overexpression context unknown"]},{"year":null,"claim":"It remains unresolved how CCDC47's three reported roles — PAT-complex chaperoning, ERAD support, and Ca2+ handling — are mechanistically integrated within the same ER protein.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model linking translocon gating to Ca2+ regulation","Direct vs. indirect basis of Ca2+ phenotypes undefined","Structural basis of ERAD partner engagement uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,6]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,3]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,2]}],"complexes":["PAT complex","multipass translocon"],"partners":["WDR83OS","SEC61","P97","BIP","DERL1","DERL2","STIM1","ORAI1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96A33","full_name":"PAT complex subunit CCDC47","aliases":["Calumin","Coiled-coil domain-containing protein 47"],"length_aa":483,"mass_kda":55.9,"function":"Component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes (PubMed:32814900, PubMed:32820719, PubMed:36261522). The MPT complex takes over after the SEC61 complex: following membrane insertion of the first few transmembrane segments of proteins by the SEC61 complex, the MPT complex occludes the lateral gate of the SEC61 complex to promote insertion of subsequent transmembrane regions (PubMed:36261522). Within the MPT complex, the PAT subcomplex sequesters any highly polar regions in the transmembrane domains away from the non-polar membrane environment until they can be buried in the interior of the fully assembled protein (By similarity). Within the PAT subcomplex, CCDC47 occludes the lateral gate of the SEC61 complex (By similarity). Involved in the regulation of calcium ion homeostasis in the ER (PubMed:30401460). Required for proper protein degradation via the ERAD (ER-associated degradation) pathway (PubMed:25009997). Has an essential role in the maintenance of ER organization during embryogenesis (By similarity)","subcellular_location":"Endoplasmic reticulum membrane; Rough endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q96A33/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CCDC47","classification":"Not Classified","n_dependent_lines":37,"n_total_lines":1208,"dependency_fraction":0.030629139072847682},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000108588","cell_line_id":"CID002038","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"EMC2","stoichiometry":10.0},{"gene":"EMC4","stoichiometry":10.0},{"gene":"EMC7","stoichiometry":10.0},{"gene":"EMC8","stoichiometry":10.0},{"gene":"PGRMC2","stoichiometry":10.0},{"gene":"SEC61B","stoichiometry":10.0},{"gene":"NCLN","stoichiometry":10.0},{"gene":"EMC10","stoichiometry":10.0},{"gene":"DERL2","stoichiometry":10.0},{"gene":"TMEM33","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID002038","total_profiled":1310},"omim":[{"mim_id":"621016","title":"NEURODEVELOPMENTAL DISORDER WITH VARIABLE FAMILIAL HYPERCHOLANEMIA; NEDFHCA","url":"https://www.omim.org/entry/621016"},{"mim_id":"618474","title":"WDR83 OPPOSITE STRAND; WDR83OS","url":"https://www.omim.org/entry/618474"},{"mim_id":"618268","title":"TRICHOHEPATONEURODEVELOPMENTAL SYNDROME; THNS","url":"https://www.omim.org/entry/618268"},{"mim_id":"618260","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 47; CCDC47","url":"https://www.omim.org/entry/618260"},{"mim_id":"607748","title":"HYPERCHOLANEMIA, FAMILIAL 1; FHCA1","url":"https://www.omim.org/entry/607748"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Endoplasmic reticulum","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CCDC47"},"hgnc":{"alias_symbol":["GK001"],"prev_symbol":[]},"alphafold":{"accession":"Q96A33","domains":[{"cath_id":"-","chopping":"139-398","consensus_level":"high","plddt":90.9318,"start":139,"end":398},{"cath_id":"1.20.5","chopping":"401-446","consensus_level":"medium","plddt":88.105,"start":401,"end":446},{"cath_id":"1.20.5","chopping":"456-483","consensus_level":"medium","plddt":78.0818,"start":456,"end":483}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96A33","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96A33-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96A33-F1-predicted_aligned_error_v6.png","plddt_mean":76.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCDC47","jax_strain_url":"https://www.jax.org/strain/search?query=CCDC47"},"sequence":{"accession":"Q96A33","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96A33.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96A33/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96A33"}},"corpus_meta":[{"pmid":"32820719","id":"PMC_32820719","title":"An ER translocon for multi-pass membrane protein biogenesis.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/32820719","citation_count":108,"is_preprint":false},{"pmid":"32814900","id":"PMC_32814900","title":"An intramembrane chaperone complex facilitates membrane protein biogenesis.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32814900","citation_count":79,"is_preprint":false},{"pmid":"36261528","id":"PMC_36261528","title":"Mechanism of an intramembrane chaperone for multipass membrane proteins.","date":"2022","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/36261528","citation_count":76,"is_preprint":false},{"pmid":"24582973","id":"PMC_24582973","title":"Genome wide DNA methylation profiling for epigenetic alteration in coronary artery disease patients.","date":"2014","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/24582973","citation_count":75,"is_preprint":false},{"pmid":"33249490","id":"PMC_33249490","title":"The genetic landscape of choroid plexus tumors in children and adults.","date":"2021","source":"Neuro-oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33249490","citation_count":40,"is_preprint":false},{"pmid":"31889940","id":"PMC_31889940","title":"The plasma peptides of breast versus ovarian cancer.","date":"2019","source":"Clinical proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/31889940","citation_count":27,"is_preprint":false},{"pmid":"30401460","id":"PMC_30401460","title":"Bi-allelic CCDC47 Variants Cause a Disorder Characterized by Woolly Hair, Liver Dysfunction, Dysmorphic Features, and Global Developmental Delay.","date":"2018","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30401460","citation_count":22,"is_preprint":false},{"pmid":"25009997","id":"PMC_25009997","title":"Contribution of calumin to embryogenesis through participation in the endoplasmic reticulum-associated degradation activity.","date":"2014","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/25009997","citation_count":15,"is_preprint":false},{"pmid":"30140426","id":"PMC_30140426","title":"Dysregulation of the calcium handling protein, CCDC47, is associated with diabetic cardiomyopathy.","date":"2018","source":"Cell & bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/30140426","citation_count":8,"is_preprint":false},{"pmid":"39553470","id":"PMC_39553470","title":"Bioinformatical analysis and experimental validation of endoplasmic reticulum stress-related biomarker genes in type 2 diabetes mellitus.","date":"2024","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39553470","citation_count":3,"is_preprint":false},{"pmid":"38524542","id":"PMC_38524542","title":"Clinical and genetic analysis of trichohepatoneurodevelopmental syndrome caused by a CCDC47 variant.","date":"2024","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/38524542","citation_count":2,"is_preprint":false},{"pmid":"28974366","id":"PMC_28974366","title":"Human CCDC47 sandwich immunoassay development with electrochemiluminescence technology.","date":"2017","source":"Journal of immunological methods","url":"https://pubmed.ncbi.nlm.nih.gov/28974366","citation_count":1,"is_preprint":false},{"pmid":"39471804","id":"PMC_39471804","title":"Homozygous variants in WDR83OS lead to a neurodevelopmental disorder with hypercholanemia.","date":"2024","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39471804","citation_count":1,"is_preprint":false},{"pmid":"41162385","id":"PMC_41162385","title":"SND3 is the membrane insertase within a distinct SEC61 translocon complex.","date":"2025","source":"Nature 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Part A","url":"https://pubmed.ncbi.nlm.nih.gov/39171352","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.07.08.663624","title":"SND3 is the membrane insertase within a fungal multipass translocon","date":"2025-07-11","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.08.663624","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11756,"output_tokens":2142,"usd":0.033699,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9144,"output_tokens":2900,"usd":0.05911,"stage2_stop_reason":"end_turn"},"total_usd":0.092809,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"CCDC47 is a component of a ~360 kDa ribosome-associated ER translocon complex (alongside Sec61, TMCO1, Nicalin, TMEM147, and NOMO) that selectively engages hundreds of multi-pass membrane protein clients; cryo-EM reveals CCDC47 as part of a large assembly at the ribosome exit tunnel organized around a central membrane cavity, and cells lacking CCDC47 show reduced levels of the multi-pass client EAAT1.\",\n      \"method\": \"Cryo-electron microscopy, high-throughput mRNA sequencing, cell-based loss-of-function (accessory component knockout)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure plus functional client-protein assay, replicated by independent lab (PMID:32814900) in the same year\",\n      \"pmids\": [\"32820719\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CCDC47 forms an obligate heterodimeric intramembrane chaperone complex (the PAT complex) with Asterix (WDR83OS product). The PAT complex engages nascent transmembrane domains containing unshielded hydrophilic side chains within the lipid bilayer and disengages upon substrate folding; cells lacking either subunit show reduced biogenesis of numerous multi-spanning membrane proteins.\",\n      \"method\": \"Co-immunoprecipitation, reconstitution of PAT complex, loss-of-function cell assays measuring multi-spanning membrane protein levels\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP establishing obligate heterodimer, functional KO phenotype across numerous substrates, independently replicated structurally (PMID:36261528)\",\n      \"pmids\": [\"32814900\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Structural and biochemical analysis of multipass protein biogenesis intermediates showed that CCDC47 occludes and latches the Sec61 lateral gate closed, preventing nascent chain engagement with Sec61; instead, Asterix binds and redirects the substrate to a position behind Sec61 within a semi-enclosed, lipid-filled cavity formed by the PAT complex and multipass translocon. Multiple TMDs are detected in this cavity after emerging from the ribosome, indicating that multipass proteins insert and fold behind Sec61.\",\n      \"method\": \"Cryo-electron microscopy, biochemical trapping of biogenesis intermediates, Sec61 lateral gate inhibitor assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure of biogenesis intermediates combined with biochemical and pharmacological orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"36261528\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Calumin (CCDC47) co-immunoprecipitates with ERAD components p97, BIP, Derlin-1, Derlin-2, and VIMP, and its knockdown in HEK293 cells reduces ERAD efficiency, as shown by attenuated degradation of misfolded α1-antitrypsin and impaired ER-to-cytosol dislocation of cholera toxin A1 subunit; loss of calumin in mouse embryos causes ER stress-associated alterations in yolk sac endoderm, contributing to embryonic lethality.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown with ERAD functional assays (misfolded protein degradation, cholera toxin dislocation), mouse knockout embryo analysis\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with multiple ERAD partners plus two orthogonal functional ERAD assays in a single study\",\n      \"pmids\": [\"25009997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Bi-allelic loss-of-function variants in CCDC47 cause reduced total ER Ca2+ storage, impaired IP3R-mediated Ca2+ release, and reduced ER Ca2+ refilling via store-operated Ca2+ entry (SOCE) in patient-derived cells, establishing CCDC47 as required for ER Ca2+ homeostasis.\",\n      \"method\": \"Patient cell characterization, Ca2+ signaling assays (ER Ca2+ store measurement, IP3R release assay, SOCE measurement), mRNA/protein quantification\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal Ca2+ assays in patient-derived cells, single lab\",\n      \"pmids\": [\"30401460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Overexpression of CCDC47 in rat H9C2 cardiomyocytes increases ionomycin-induced Ca2+ release and reuptake, demonstrating a positive role for CCDC47 in ER/SR Ca2+ handling in cardiomyocytes.\",\n      \"method\": \"Overexpression in rat cardiomyocyte cell line, ionomycin-induced Ca2+ release/reuptake assay\",\n      \"journal\": \"Cell & bioscience\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single overexpression experiment in a cell line, single lab, single method\",\n      \"pmids\": [\"30140426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a fungal (Chaetomium thermophilum) SND3 translocon cryo-EM structure, CCDC47 is present alongside SEC61 and TRAPα; the SEC61β N-terminus works together with CCDC47 to prevent substrate access to the SEC61 translocon within this SND pathway complex.\",\n      \"method\": \"Cryo-electron microscopy of ribosome-associated SND3 translocon complex\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — cryo-EM structure establishes CCDC47 position and role in gating, but single study in a fungal ortholog context\",\n      \"pmids\": [\"41162385\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CCDC47 co-immunoprecipitates with pancreas-specific SPCA2C (Atp2c2c) and with STIM1 and Orai1; co-expression of CCDC47 and SPCA2C increases store-operated Ca2+ entry (SOCE) and resting cytosolic Ca2+ above either protein alone. These interactions depend on the CCDC47 coiled-coil domain or accessible transmembrane domains.\",\n      \"method\": \"Co-immunoprecipitation, co-localization microscopy, co-expression functional SOCE assay in HEK-Orai1YFP cells, domain-deletion experiments\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and functional co-expression assay with domain-deletion mapping, single lab\",\n      \"pmids\": [\"40783819\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCDC47 is an ER-resident transmembrane protein that functions primarily as the obligate partner of Asterix in the PAT intramembrane chaperone complex, which occludes the Sec61 lateral gate and redirects nascent hydrophilic transmembrane domains to a lipid-filled cavity behind Sec61 for co-translational folding of multi-pass membrane proteins; it additionally participates in ERAD through interactions with p97, BIP, and Derlin family proteins, and contributes to ER Ca2+ homeostasis by supporting IP3R-mediated Ca2+ release and store-operated Ca2+ entry.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CCDC47 is an ER-resident component of the ribosome-associated multipass translocon that governs the co-translational biogenesis of multi-spanning membrane proteins [#0]. It functions as the obligate heterodimeric partner of Asterix (WDR83OS) in the PAT intramembrane chaperone complex, which engages nascent transmembrane domains bearing unshielded hydrophilic side chains within the bilayer and disengages once the substrate folds; loss of either subunit reduces the biogenesis of numerous multi-spanning membrane proteins [#1]. Mechanistically, CCDC47 occludes and latches the Sec61 lateral gate closed, while Asterix captures the substrate and redirects it to a semi-enclosed, lipid-filled cavity behind Sec61 where multiple TMDs insert and fold [#2]; a gating role for CCDC47 in restricting Sec61 access is structurally conserved in a fungal SND translocon [#6]. Independently of this chaperone role, CCDC47 participates in ER-associated degradation, co-immunoprecipitating with p97, BIP, Derlin-1, Derlin-2, and VIMP and supporting misfolded-protein turnover and ER-to-cytosol dislocation [#3], and it is required for ER Ca2+ homeostasis, with bi-allelic loss-of-function variants in patients impairing ER Ca2+ storage, IP3R-mediated release, and store-operated Ca2+ entry [#4]. Loss of CCDC47 in mouse embryos causes ER stress and embryonic lethality [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established the first molecular role for CCDC47 (calumin) by placing it in the ERAD machinery, addressing what cellular process this ER protein serves.\",\n      \"evidence\": \"Co-IP with p97/BIP/Derlin-1/Derlin-2/VIMP plus ERAD functional assays and knockout mouse embryo analysis\",\n      \"pmids\": [\"25009997\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether CCDC47 acts directly in dislocation or as a scaffold\", \"No structural basis for the ERAD partner interactions\", \"Relationship to its later-defined chaperone role left undefined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Linked CCDC47 to ER Ca2+ homeostasis in humans, showing its loss disrupts Ca2+ storage and signaling and answering whether CCDC47 dysfunction has a physiological/clinical consequence.\",\n      \"evidence\": \"Patient-derived cells with bi-allelic loss-of-function variants assayed for ER Ca2+ stores, IP3R release, and SOCE\",\n      \"pmids\": [\"30401460\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting CCDC47 to IP3R and SOCE machinery not defined\", \"Single lab\", \"Whether Ca2+ defects are direct or secondary to translocon/ERAD dysfunction unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Provided a gain-of-function correlate for the Ca2+ role, showing CCDC47 overexpression enhances cardiomyocyte Ca2+ release and reuptake.\",\n      \"evidence\": \"CCDC47 overexpression in rat H9C2 cells with ionomycin-induced Ca2+ assay\",\n      \"pmids\": [\"30140426\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single overexpression experiment in one cell line and method\", \"No mechanistic interaction established\", \"Not validated by loss-of-function\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Defined CCDC47 as a constituent of a large ribosome-associated multipass translocon selective for multi-spanning clients, reframing it as a biogenesis factor.\",\n      \"evidence\": \"Cryo-EM of the ~360 kDa translocon, client mRNA-seq profiling, and knockout reducing the multi-pass client EAAT1\",\n      \"pmids\": [\"32820719\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define CCDC47's specific molecular action within the assembly\", \"Mechanism of client selectivity unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified the obligate CCDC47–Asterix PAT heterodimer as an intramembrane chaperone that engages unshielded TMDs, establishing the molecular function underlying multipass biogenesis.\",\n      \"evidence\": \"Reciprocal Co-IP, PAT complex reconstitution, and loss-of-function assays across many multi-spanning substrates\",\n      \"pmids\": [\"32814900\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not yet show the structural mechanism of substrate handoff\", \"Division of labor between CCDC47 and Asterix not resolved at this stage\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolved the mechanism of action: CCDC47 latches the Sec61 lateral gate closed while Asterix redirects substrates into a lipid-filled cavity behind Sec61 for folding.\",\n      \"evidence\": \"Cryo-EM of trapped biogenesis intermediates with biochemical trapping and Sec61 lateral-gate inhibitor assays\",\n      \"pmids\": [\"36261528\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics and kinetics of gate latching not quantified\", \"How specific TMD features trigger PAT engagement/release not fully defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed CCDC47-mediated gating of the Sec61 translocon is conserved in a fungal SND-pathway translocon, generalizing the latching role.\",\n      \"evidence\": \"Cryo-EM of the Chaetomium thermophilum SND3 translocon with SEC61 and TRAPα\",\n      \"pmids\": [\"41162385\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single study in a fungal ortholog\", \"Functional consequence of SND-context gating not assayed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected CCDC47 physically to SOCE machinery, identifying SPCA2C, STIM1, and Orai1 partners and a domain dependence for Ca2+ enhancement.\",\n      \"evidence\": \"Co-IP, co-localization, co-expression SOCE assays in HEK-Orai1 cells, and domain-deletion mapping to the coiled-coil/TM regions\",\n      \"pmids\": [\"40783819\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Whether interactions are direct vs. complex-mediated not established\", \"Physiological relevance beyond overexpression context unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how CCDC47's three reported roles — PAT-complex chaperoning, ERAD support, and Ca2+ handling — are mechanistically integrated within the same ER protein.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model linking translocon gating to Ca2+ regulation\", \"Direct vs. indirect basis of Ca2+ phenotypes undefined\", \"Structural basis of ERAD partner engagement uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [\"PAT complex\", \"multipass translocon\"],\n    \"partners\": [\"WDR83OS\", \"SEC61\", \"p97\", \"BIP\", \"DERL1\", \"DERL2\", \"STIM1\", \"ORAI1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}