{"gene":"EMC4","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2020,"finding":"Cryo-EM structure of the yeast EMC revealed that Emc4's transmembrane domain tilts away from the main transmembrane region and is partially mobile. Mutational studies demonstrated that the flexibility of Emc4 is required for EMC function in TMH insertion.","method":"Cryo-EM structure determination + mutagenesis functional assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure combined with mutagenesis validating functional requirement for Emc4 flexibility","pmids":["32494008"],"is_preprint":false},{"year":2020,"finding":"EMC4 (together with EMC7) supports SV40 polyomavirus infection by promoting late-endosome (LE)-to-ER targeting of the virus. EMC4 engages LE-associated Rab7 (presumably to stabilize LE-ER membrane contact) and binds ER-resident syntaxin18, a fusion machinery component required for SV40 arrival at the ER.","method":"Co-immunoprecipitation (EMC4 binding to Rab7 and syntaxin18), siRNA knockdown of EMC subunits with infection assays, intracellular trafficking readouts","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP for binding partners plus functional KD phenotype, single lab","pmids":["32111841"],"is_preprint":false},{"year":2022,"finding":"EMC4 promotes fusion of DENV and endosomal membranes during viral entry, enabling cytosolic genome delivery. EMC4 also mediates ER-to-endosome transfer of phosphatidylserine, whose endosomal presence facilitates DENV-endosomal membrane fusion.","method":"siRNA knockdown of EMC4 with DENV infection and fusion assays; phosphatidylserine transfer assay","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined cellular phenotype (loss-of-function) with two distinct mechanistic readouts (fusion and lipid transfer), single lab","pmids":["35834589"],"is_preprint":false},{"year":2008,"finding":"Human TMEM85 (EMC4) heterologously expressed in yeast promotes growth and prevents cell death in response to oxidative stress (H2O2). The yeast ortholog YGL231c has the same protective effect, indicating a conserved anti-apoptotic function.","method":"Heterologous expression in S. cerevisiae; growth and viability assays under oxidative stress","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined loss/gain-of-function phenotype with replicated finding across human and yeast orthologs; single lab","pmids":["18586032"],"is_preprint":false},{"year":2019,"finding":"TMEM85 (EMC4) physically interacts with both GLUT9a and GLUT9b urate transporter isoforms, confirmed by co-immunoprecipitation in HEK 293T cells and Xenopus oocytes; however, co-expression of TMEM85 did not inhibit GLUT9-mediated urate uptake (negative functional result).","method":"Dual-membrane yeast two-hybrid screen for identification; co-immunoprecipitation in HEK 293T cells and Xenopus oocytes for confirmation; urate transport functional assay","journal":"Frontiers in physiology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP confirmed physical interaction in two systems; functional assay showed no effect on urate transport","pmids":["31695625"],"is_preprint":false},{"year":2020,"finding":"Overexpression of full-length yeast EMC4 (Emc4p) suppresses slow-growth and general control derepression phenotypes caused by eIF2Bβ (gcd7-201) and eIF2Bγ (gcd1-502) mutations in S. cerevisiae, placing Emc4p as a genetic suppressor of eIF2B-mediated translational control defects. Emc4p overexpression also conferred resistance to H2O2, ethanol, and caffeine stress in both wild-type and mutant strains.","method":"High-copy suppressor screen; sub-cloning and overexpression in eIF2B mutant yeast strains; western blotting for GST-Emc4 fusion; growth/phenotype assays","journal":"Journal, genetic engineering & biotechnology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — genetic epistasis (suppressor) and growth assays in yeast, single lab, no direct biochemical mechanism established","pmids":["32476094"],"is_preprint":false},{"year":2025,"finding":"CRISPR-mediated ablation of EMC4 in HEK293 cells and human iPSC-derived neurons reduces pSer129-αSynuclein aggregation across multiple αSyn polymorphs by enhancing ER-driven autophagic flux and lysosomal clearance.","method":"Arrayed CRISPR knockout screen; high-throughput fluorescence microscopy for pSyn129; autophagic flux and lysosomal clearance assays; validated in iPSC-derived neurons","journal":"FEBS open bio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic CRISPR screen with defined cellular mechanism, replicated in iPSC neurons; single lab but multiple orthogonal readouts","pmids":["41911287"],"is_preprint":false}],"current_model":"EMC4 is a partially mobile transmembrane subunit of the ER membrane complex (EMC) insertase whose structural flexibility is required for co-translational TMH insertion; beyond its core insertase role, EMC4 acts as a molecular tether linking the ER to late endosomes via Rab7 and syntaxin18 interactions, mediates ER-to-endosome phosphatidylserine transfer to facilitate viral membrane fusion, protects against oxidative-stress-induced cell death, physically interacts with the GLUT9 urate transporter without functionally regulating urate transport, and its ablation reduces α-synuclein aggregation by enhancing ER-driven autophagic/lysosomal clearance."},"narrative":{"mechanistic_narrative":"EMC4 (TMEM85) is a transmembrane subunit of the ER membrane complex (EMC) insertase, where its transmembrane domain tilts away from the main transmembrane region and remains partially mobile; this structural flexibility is functionally required for the EMC to insert transmembrane helices into the ER membrane [PMID:32494008]. Beyond its core insertase role, EMC4 functions at ER–endosome interfaces: it engages late-endosome-associated Rab7 and binds ER-resident syntaxin18 to support late-endosome-to-ER targeting of SV40 polyomavirus [PMID:32111841], and it mediates ER-to-endosome transfer of phosphatidylserine that promotes fusion of dengue virus with endosomal membranes during viral entry [PMID:35834589]. Heterologous expression studies establish a conserved cytoprotective function, with EMC4 promoting growth and viability under oxidative stress [PMID:18586032]. EMC4 physically interacts with the GLUT9 urate transporter isoforms but does not regulate urate uptake [PMID:31695625], and its ablation reduces α-synuclein aggregation by enhancing ER-driven autophagic flux and lysosomal clearance [PMID:41911287].","teleology":[{"year":2008,"claim":"Established the first functional readout for EMC4 by showing it confers cytoprotection, revealing a conserved role in the oxidative stress response.","evidence":"Heterologous expression of human TMEM85 and its yeast ortholog in S. cerevisiae with viability assays under H2O2 stress","pmids":["18586032"],"confidence":"Medium","gaps":["No molecular mechanism linking EMC4 to oxidative-stress protection identified","Did not connect protective effect to EMC insertase activity"]},{"year":2019,"claim":"Identified a direct physical partner of EMC4 (GLUT9) while delineating the boundary of its function, showing binding does not equate to transport regulation.","evidence":"Dual-membrane yeast two-hybrid screen, co-IP in HEK293T and Xenopus oocytes, and urate transport assays","pmids":["31695625"],"confidence":"Medium","gaps":["Functional consequence of the EMC4–GLUT9 interaction unknown","No structural basis for the interaction defined"]},{"year":2020,"claim":"Defined the structural mechanism of EMC4 within the insertase, establishing that its transmembrane flexibility is essential for transmembrane helix insertion.","evidence":"Cryo-EM structure of the yeast EMC combined with mutagenesis functional assays","pmids":["32494008"],"confidence":"High","gaps":["Substrate specificity contributed by EMC4 not resolved","How EMC4 mobility couples to the catalytic cycle not detailed"]},{"year":2020,"claim":"Extended EMC4 function beyond insertase activity to membrane tethering, showing it bridges late endosomes and ER via Rab7 and syntaxin18 to support viral trafficking.","evidence":"Co-IP of EMC4 with Rab7 and syntaxin18, plus siRNA knockdown with SV40 infection and trafficking readouts","pmids":["32111841"],"confidence":"Medium","gaps":["Whether tethering is independent of the full EMC complex unclear","Single lab; physiological (non-viral) role of the contact site untested"]},{"year":2020,"claim":"Placed EMC4 as a genetic suppressor of eIF2B-mediated translational control defects, linking it to stress-response phenotypes.","evidence":"High-copy suppressor screen and overexpression in eIF2B mutant yeast with growth/phenotype assays","pmids":["32476094"],"confidence":"Low","gaps":["Genetic epistasis only; no direct biochemical mechanism established","Connection to eIF2B translational control is indirect","Not validated in mammalian cells"]},{"year":2022,"claim":"Defined a lipid-transfer mechanism for EMC4, showing it moves phosphatidylserine from ER to endosomes to enable viral membrane fusion.","evidence":"siRNA knockdown of EMC4 with DENV infection/fusion assays and phosphatidylserine transfer assays","pmids":["35834589"],"confidence":"Medium","gaps":["Direct lipid-transfer activity of EMC4 versus indirect facilitation not distinguished","Single lab; structural basis of PS transfer unknown"]},{"year":2025,"claim":"Connected EMC4 to proteostasis, showing its loss reduces α-synuclein aggregation by boosting ER-driven autophagic and lysosomal clearance.","evidence":"Arrayed CRISPR knockout screen in HEK293 and iPSC-derived neurons with pSyn129 microscopy, autophagic flux and lysosomal clearance assays","pmids":["41911287"],"confidence":"Medium","gaps":["Molecular link between EMC4 ablation and enhanced autophagic flux not defined","Whether the effect requires EMC insertase activity unknown"]},{"year":null,"claim":"How EMC4's core insertase function mechanistically connects to its tethering, lipid-transfer, cytoprotective, and proteostasis roles remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No single mechanism unifies the distinct EMC4 activities","Unclear which functions require the intact EMC versus EMC4 alone"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[6]}],"complexes":["ER membrane complex (EMC)"],"partners":["RAB7","STX18","GLUT9","EMC7"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5J8M3","full_name":"ER membrane protein complex subunit 4","aliases":["Cell proliferation-inducing gene 17 protein","Transmembrane protein 85"],"length_aa":183,"mass_kda":20.1,"function":"Part of the endoplasmic reticulum membrane protein complex (EMC) that enables the energy-independent insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins (PubMed:29242231, PubMed:29809151, PubMed:30415835, PubMed:32439656, PubMed:32459176). Preferentially accommodates proteins with transmembrane domains that are weakly hydrophobic or contain destabilizing features such as charged and aromatic residues (PubMed:29242231, PubMed:29809151, PubMed:30415835). Involved in the cotranslational insertion of multi-pass membrane proteins in which stop-transfer membrane-anchor sequences become ER membrane spanning helices (PubMed:29809151, PubMed:30415835). It is also required for the post-translational insertion of tail-anchored/TA proteins in endoplasmic reticulum membranes (PubMed:29242231, PubMed:29809151). By mediating the proper cotranslational insertion of N-terminal transmembrane domains in an N-exo topology, with translocated N-terminus in the lumen of the ER, controls the topology of multi-pass membrane proteins like the G protein-coupled receptors (PubMed:30415835). By regulating the insertion of various proteins in membranes, it is indirectly involved in many cellular processes (Probable)","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q5J8M3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/EMC4","classification":"Common Essential","n_dependent_lines":657,"n_total_lines":1208,"dependency_fraction":0.5438741721854304},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000128463","cell_line_id":"CID001791","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"EMC1","stoichiometry":10.0},{"gene":"EMC2","stoichiometry":10.0},{"gene":"EMC3","stoichiometry":10.0},{"gene":"EMC7","stoichiometry":10.0},{"gene":"CCDC47","stoichiometry":10.0},{"gene":"EMC8","stoichiometry":10.0},{"gene":"EMC9","stoichiometry":4.0},{"gene":"EMC10","stoichiometry":0.2},{"gene":"RPL11","stoichiometry":0.2},{"gene":"MMGT1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001791","total_profiled":1310},"omim":[{"mim_id":"620631","title":"ENDOPLASMIC RETICULUM MEMBRANE PROTEIN COMPLEX, SUBUNIT 7; EMC7","url":"https://www.omim.org/entry/620631"},{"mim_id":"620261","title":"ENDOPLASMIC RETICULUM MEMBRANE PROTEIN COMPLEX, SUBUNIT 6; EMC6","url":"https://www.omim.org/entry/620261"},{"mim_id":"616245","title":"ENDOPLASMIC RETICULUM MEMBRANE PROTEIN COMPLEX, SUBUNIT 4; EMC4","url":"https://www.omim.org/entry/616245"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/EMC4"},"hgnc":{"alias_symbol":["FLJ90746","MGC24415","PIG17"],"prev_symbol":["TMEM85"]},"alphafold":{"accession":"Q5J8M3","domains":[{"cath_id":"-","chopping":"54-158","consensus_level":"high","plddt":72.1599,"start":54,"end":158}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5J8M3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5J8M3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5J8M3-F1-predicted_aligned_error_v6.png","plddt_mean":66.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EMC4","jax_strain_url":"https://www.jax.org/strain/search?query=EMC4"},"sequence":{"accession":"Q5J8M3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5J8M3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5J8M3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5J8M3"}},"corpus_meta":[{"pmid":"32494008","id":"PMC_32494008","title":"Structure of the ER membrane complex, a transmembrane-domain insertase.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32494008","citation_count":110,"is_preprint":false},{"pmid":"1939214","id":"PMC_1939214","title":"Short chain collagens in sponges are encoded by a family of closely related genes.","date":"1991","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1939214","citation_count":49,"is_preprint":false},{"pmid":"2163843","id":"PMC_2163843","title":"Cloning and sequencing of a Porifera partial cDNA coding for a short-chain collagen.","date":"1990","source":"European journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/2163843","citation_count":39,"is_preprint":false},{"pmid":"28342328","id":"PMC_28342328","title":"Reproductive toxicity of β-diketone antibiotic mixtures to zebrafish (Danio rerio).","date":"2017","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/28342328","citation_count":28,"is_preprint":false},{"pmid":"31695625","id":"PMC_31695625","title":"Interaction Between ITM2B and GLUT9 Links Urate Transport to Neurodegenerative Disorders.","date":"2019","source":"Frontiers in physiology","url":"https://pubmed.ncbi.nlm.nih.gov/31695625","citation_count":22,"is_preprint":false},{"pmid":"32111841","id":"PMC_32111841","title":"Selective EMC subunits act as molecular tethers of intracellular organelles exploited during viral entry.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32111841","citation_count":22,"is_preprint":false},{"pmid":"29069762","id":"PMC_29069762","title":"Cell lines generated from a chronic lymphocytic leukemia mouse model exhibit constitutive Btk and Akt signaling.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29069762","citation_count":17,"is_preprint":false},{"pmid":"18586032","id":"PMC_18586032","title":"Transmembrane protein 85 from both human (TMEM85) and yeast (YGL231c) inhibit hydrogen peroxide mediated cell death in yeast.","date":"2008","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/18586032","citation_count":15,"is_preprint":false},{"pmid":"33719335","id":"PMC_33719335","title":"Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder.","date":"2021","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33719335","citation_count":8,"is_preprint":false},{"pmid":"35834589","id":"PMC_35834589","title":"A specific EMC subunit supports Dengue virus infection by promoting virus membrane fusion essential for cytosolic genome delivery.","date":"2022","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/35834589","citation_count":6,"is_preprint":false},{"pmid":"32661467","id":"PMC_32661467","title":"Identifying specific miRNAs and associated mRNAs in CD44 and CD90 cancer stem cell subtypes in gastric cancer cell line SNU-5.","date":"2020","source":"International journal of clinical and experimental pathology","url":"https://pubmed.ncbi.nlm.nih.gov/32661467","citation_count":5,"is_preprint":false},{"pmid":"32476094","id":"PMC_32476094","title":"Saccharomyces cerevisiae ER membrane protein complex subunit 4 (EMC4) plays a crucial role in eIF2B-mediated translation regulation and survival under stress conditions.","date":"2020","source":"Journal, genetic engineering & biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/32476094","citation_count":3,"is_preprint":false},{"pmid":"35281346","id":"PMC_35281346","title":"Analysis of Potential Hub Genes for Neuropathic Pain Based on Differential Expression in Rat Models.","date":"2022","source":"Pain research & management","url":"https://pubmed.ncbi.nlm.nih.gov/35281346","citation_count":3,"is_preprint":false},{"pmid":"28677085","id":"PMC_28677085","title":"Role of Saccharomyces cerevisiae TAN1 (tRNA acetyltransferase) in eukaryotic initiation factor 2B (eIF2B)-mediated translation control and stress response.","date":"2017","source":"3 Biotech","url":"https://pubmed.ncbi.nlm.nih.gov/28677085","citation_count":1,"is_preprint":false},{"pmid":"41911287","id":"PMC_41911287","title":"Large-scale bidirectional arrayed genetic screens identify OXR1 and EMC4 as modifiers of αSynuclein aggregation.","date":"2026","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/41911287","citation_count":0,"is_preprint":false},{"pmid":"40674570","id":"PMC_40674570","title":"A multi-omic analysis to investigate the causal associations between circulating proteins and risk of spontaneous abortion and their potential implications.","date":"2025","source":"JBRA assisted reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/40674570","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.10.658866","title":"Large-scale bidirectional arrayed genetic screens identify  <i>OXR1</i>  and  <i>EMC4</i>  as modifiers of α-synuclein aggregation","date":"2025-06-11","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.10.658866","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10532,"output_tokens":1810,"usd":0.029373,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8650,"output_tokens":2398,"usd":0.0516,"stage2_stop_reason":"end_turn"},"total_usd":0.080973,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"Cryo-EM structure of the yeast EMC revealed that Emc4's transmembrane domain tilts away from the main transmembrane region and is partially mobile. Mutational studies demonstrated that the flexibility of Emc4 is required for EMC function in TMH insertion.\",\n      \"method\": \"Cryo-EM structure determination + mutagenesis functional assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure combined with mutagenesis validating functional requirement for Emc4 flexibility\",\n      \"pmids\": [\"32494008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"EMC4 (together with EMC7) supports SV40 polyomavirus infection by promoting late-endosome (LE)-to-ER targeting of the virus. EMC4 engages LE-associated Rab7 (presumably to stabilize LE-ER membrane contact) and binds ER-resident syntaxin18, a fusion machinery component required for SV40 arrival at the ER.\",\n      \"method\": \"Co-immunoprecipitation (EMC4 binding to Rab7 and syntaxin18), siRNA knockdown of EMC subunits with infection assays, intracellular trafficking readouts\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP for binding partners plus functional KD phenotype, single lab\",\n      \"pmids\": [\"32111841\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"EMC4 promotes fusion of DENV and endosomal membranes during viral entry, enabling cytosolic genome delivery. EMC4 also mediates ER-to-endosome transfer of phosphatidylserine, whose endosomal presence facilitates DENV-endosomal membrane fusion.\",\n      \"method\": \"siRNA knockdown of EMC4 with DENV infection and fusion assays; phosphatidylserine transfer assay\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined cellular phenotype (loss-of-function) with two distinct mechanistic readouts (fusion and lipid transfer), single lab\",\n      \"pmids\": [\"35834589\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human TMEM85 (EMC4) heterologously expressed in yeast promotes growth and prevents cell death in response to oxidative stress (H2O2). The yeast ortholog YGL231c has the same protective effect, indicating a conserved anti-apoptotic function.\",\n      \"method\": \"Heterologous expression in S. cerevisiae; growth and viability assays under oxidative stress\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined loss/gain-of-function phenotype with replicated finding across human and yeast orthologs; single lab\",\n      \"pmids\": [\"18586032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TMEM85 (EMC4) physically interacts with both GLUT9a and GLUT9b urate transporter isoforms, confirmed by co-immunoprecipitation in HEK 293T cells and Xenopus oocytes; however, co-expression of TMEM85 did not inhibit GLUT9-mediated urate uptake (negative functional result).\",\n      \"method\": \"Dual-membrane yeast two-hybrid screen for identification; co-immunoprecipitation in HEK 293T cells and Xenopus oocytes for confirmation; urate transport functional assay\",\n      \"journal\": \"Frontiers in physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP confirmed physical interaction in two systems; functional assay showed no effect on urate transport\",\n      \"pmids\": [\"31695625\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Overexpression of full-length yeast EMC4 (Emc4p) suppresses slow-growth and general control derepression phenotypes caused by eIF2Bβ (gcd7-201) and eIF2Bγ (gcd1-502) mutations in S. cerevisiae, placing Emc4p as a genetic suppressor of eIF2B-mediated translational control defects. Emc4p overexpression also conferred resistance to H2O2, ethanol, and caffeine stress in both wild-type and mutant strains.\",\n      \"method\": \"High-copy suppressor screen; sub-cloning and overexpression in eIF2B mutant yeast strains; western blotting for GST-Emc4 fusion; growth/phenotype assays\",\n      \"journal\": \"Journal, genetic engineering & biotechnology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — genetic epistasis (suppressor) and growth assays in yeast, single lab, no direct biochemical mechanism established\",\n      \"pmids\": [\"32476094\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRISPR-mediated ablation of EMC4 in HEK293 cells and human iPSC-derived neurons reduces pSer129-αSynuclein aggregation across multiple αSyn polymorphs by enhancing ER-driven autophagic flux and lysosomal clearance.\",\n      \"method\": \"Arrayed CRISPR knockout screen; high-throughput fluorescence microscopy for pSyn129; autophagic flux and lysosomal clearance assays; validated in iPSC-derived neurons\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic CRISPR screen with defined cellular mechanism, replicated in iPSC neurons; single lab but multiple orthogonal readouts\",\n      \"pmids\": [\"41911287\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EMC4 is a partially mobile transmembrane subunit of the ER membrane complex (EMC) insertase whose structural flexibility is required for co-translational TMH insertion; beyond its core insertase role, EMC4 acts as a molecular tether linking the ER to late endosomes via Rab7 and syntaxin18 interactions, mediates ER-to-endosome phosphatidylserine transfer to facilitate viral membrane fusion, protects against oxidative-stress-induced cell death, physically interacts with the GLUT9 urate transporter without functionally regulating urate transport, and its ablation reduces α-synuclein aggregation by enhancing ER-driven autophagic/lysosomal clearance.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EMC4 (TMEM85) is a transmembrane subunit of the ER membrane complex (EMC) insertase, where its transmembrane domain tilts away from the main transmembrane region and remains partially mobile; this structural flexibility is functionally required for the EMC to insert transmembrane helices into the ER membrane [#0]. Beyond its core insertase role, EMC4 functions at ER–endosome interfaces: it engages late-endosome-associated Rab7 and binds ER-resident syntaxin18 to support late-endosome-to-ER targeting of SV40 polyomavirus [#1], and it mediates ER-to-endosome transfer of phosphatidylserine that promotes fusion of dengue virus with endosomal membranes during viral entry [#2]. Heterologous expression studies establish a conserved cytoprotective function, with EMC4 promoting growth and viability under oxidative stress [#3]. EMC4 physically interacts with the GLUT9 urate transporter isoforms but does not regulate urate uptake [#4], and its ablation reduces α-synuclein aggregation by enhancing ER-driven autophagic flux and lysosomal clearance [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established the first functional readout for EMC4 by showing it confers cytoprotection, revealing a conserved role in the oxidative stress response.\",\n      \"evidence\": \"Heterologous expression of human TMEM85 and its yeast ortholog in S. cerevisiae with viability assays under H2O2 stress\",\n      \"pmids\": [\"18586032\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular mechanism linking EMC4 to oxidative-stress protection identified\", \"Did not connect protective effect to EMC insertase activity\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified a direct physical partner of EMC4 (GLUT9) while delineating the boundary of its function, showing binding does not equate to transport regulation.\",\n      \"evidence\": \"Dual-membrane yeast two-hybrid screen, co-IP in HEK293T and Xenopus oocytes, and urate transport assays\",\n      \"pmids\": [\"31695625\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the EMC4–GLUT9 interaction unknown\", \"No structural basis for the interaction defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Defined the structural mechanism of EMC4 within the insertase, establishing that its transmembrane flexibility is essential for transmembrane helix insertion.\",\n      \"evidence\": \"Cryo-EM structure of the yeast EMC combined with mutagenesis functional assays\",\n      \"pmids\": [\"32494008\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate specificity contributed by EMC4 not resolved\", \"How EMC4 mobility couples to the catalytic cycle not detailed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended EMC4 function beyond insertase activity to membrane tethering, showing it bridges late endosomes and ER via Rab7 and syntaxin18 to support viral trafficking.\",\n      \"evidence\": \"Co-IP of EMC4 with Rab7 and syntaxin18, plus siRNA knockdown with SV40 infection and trafficking readouts\",\n      \"pmids\": [\"32111841\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether tethering is independent of the full EMC complex unclear\", \"Single lab; physiological (non-viral) role of the contact site untested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed EMC4 as a genetic suppressor of eIF2B-mediated translational control defects, linking it to stress-response phenotypes.\",\n      \"evidence\": \"High-copy suppressor screen and overexpression in eIF2B mutant yeast with growth/phenotype assays\",\n      \"pmids\": [\"32476094\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Genetic epistasis only; no direct biochemical mechanism established\", \"Connection to eIF2B translational control is indirect\", \"Not validated in mammalian cells\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined a lipid-transfer mechanism for EMC4, showing it moves phosphatidylserine from ER to endosomes to enable viral membrane fusion.\",\n      \"evidence\": \"siRNA knockdown of EMC4 with DENV infection/fusion assays and phosphatidylserine transfer assays\",\n      \"pmids\": [\"35834589\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct lipid-transfer activity of EMC4 versus indirect facilitation not distinguished\", \"Single lab; structural basis of PS transfer unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected EMC4 to proteostasis, showing its loss reduces α-synuclein aggregation by boosting ER-driven autophagic and lysosomal clearance.\",\n      \"evidence\": \"Arrayed CRISPR knockout screen in HEK293 and iPSC-derived neurons with pSyn129 microscopy, autophagic flux and lysosomal clearance assays\",\n      \"pmids\": [\"41911287\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between EMC4 ablation and enhanced autophagic flux not defined\", \"Whether the effect requires EMC insertase activity unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How EMC4's core insertase function mechanistically connects to its tethering, lipid-transfer, cytoprotective, and proteostasis roles remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No single mechanism unifies the distinct EMC4 activities\", \"Unclear which functions require the intact EMC versus EMC4 alone\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"ER membrane complex (EMC)\"],\n    \"partners\": [\"RAB7\", \"STX18\", \"GLUT9\", \"EMC7\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":4,"faith_total":4,"faith_pct":100.0}}