{"gene":"SNRNP48","run_date":"2026-06-10T07:46:37","timeline":{"discoveries":[{"year":2025,"finding":"Cryo-EM reconstruction of the 13-subunit human U11 snRNP complex revealed that SNRNP48 is positioned near the 5' end of U11 snRNA, where it stabilizes binding of the incoming 5' splice site (5'SS). PDCD7 bridges SNRNP25 and SNRNP48, which are located at distal ends of the particle.","method":"Cryo-EM structural reconstruction of the human U11 snRNP in apo and substrate-bound forms","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with both apo and substrate-bound states, directly resolving protein positions and interactions within the complex in a single rigorous study","pmids":["39809272"],"is_preprint":false},{"year":2025,"finding":"SNRNP48 and ZMAT5 cooperate to stabilize binding of the incoming U12-type 5' splice site to the U11 snRNP, contributing to 5'SS recognition by the minor spliceosome.","method":"Cryo-EM structural analysis of substrate-bound U11 snRNP complex","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct structural visualization of SNRNP48 in substrate-bound conformation, single rigorous study with multiple structural states","pmids":["39809272"],"is_preprint":false}],"current_model":"SNRNP48 is a component of the human U11 snRNP complex of the minor spliceosome, where it localizes near the 5' end of U11 snRNA, is bridged to SNRNP25 via PDCD7, and cooperates with ZMAT5 to stabilize recognition of the U12-type 5' splice site through direct structural contacts."},"narrative":{"mechanistic_narrative":"SNRNP48 is a protein component of the human U11 snRNP of the minor spliceosome, where it participates in recognition of U12-type 5' splice sites [PMID:39809272]. Within the 13-subunit U11 particle, SNRNP48 is positioned near the 5' end of the U11 snRNA and stabilizes binding of the incoming 5' splice site, with PDCD7 bridging SNRNP48 to SNRNP25 across distal ends of the particle [PMID:39809272]. SNRNP48 acts together with ZMAT5 to stabilize engagement of the U12-type 5' splice site, contributing directly to splice-site recognition by the minor spliceosome [PMID:39809272]. Beyond its structural role in the U11 snRNP defined by cryo-EM, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2025,"claim":"The architecture of the human U11 snRNP and the spatial position of SNRNP48 within it were unknown; resolving the complex established where SNRNP48 sits and how it connects to other subunits.","evidence":"Cryo-EM reconstruction of the 13-subunit human U11 snRNP in apo and substrate-bound forms","pmids":["39809272"],"confidence":"High","gaps":["Functional consequence of SNRNP48 loss on minor-spliceosome activity not tested","Whether the PDCD7-bridged arrangement is dynamic during the splicing cycle is unresolved"]},{"year":2025,"claim":"How the minor spliceosome stabilizes the U12-type 5' splice site was unclear; structural analysis showed SNRNP48 and ZMAT5 cooperate to secure this contact.","evidence":"Cryo-EM structural analysis of the substrate-bound U11 snRNP","pmids":["39809272"],"confidence":"High","gaps":["Quantitative contribution of SNRNP48 versus ZMAT5 to splice-site affinity not separated","No mutational dissection of the residues mediating 5'SS stabilization"]},{"year":null,"claim":"Whether SNRNP48 has roles beyond the U11 snRNP, and the phenotypic effect of its disruption, remain undefined.","evidence":"","pmids":[],"confidence":"High","gaps":["No loss-of-function or depletion studies in the corpus","No disease association documented","No biochemical activity assigned beyond structural participation"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]}],"localization":[],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1]}],"complexes":["U11 snRNP","minor spliceosome"],"partners":["PDCD7","SNRNP25","ZMAT5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6IEG0","full_name":"U11/U12 small nuclear ribonucleoprotein 48 kDa protein","aliases":[],"length_aa":339,"mass_kda":40.0,"function":"Likely involved in U12-type 5' splice site recognition","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q6IEG0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SNRNP48","classification":"Not Classified","n_dependent_lines":516,"n_total_lines":1208,"dependency_fraction":0.4271523178807947},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ELOVL6","stoichiometry":0.2},{"gene":"SF3B1","stoichiometry":0.2},{"gene":"SF3B6","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPD2","stoichiometry":0.2},{"gene":"SNRPF","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/SNRNP48","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SNRNP48"},"hgnc":{"alias_symbol":["FLJ32234","dJ512B11.2","dJ336K20B.1"],"prev_symbol":["C6orf151"]},"alphafold":{"accession":"Q6IEG0","domains":[{"cath_id":"-","chopping":"56-93","consensus_level":"high","plddt":87.3208,"start":56,"end":93},{"cath_id":"-","chopping":"104-179","consensus_level":"high","plddt":82.623,"start":104,"end":179},{"cath_id":"-","chopping":"191-241","consensus_level":"medium","plddt":72.12,"start":191,"end":241},{"cath_id":"1.20.5","chopping":"9-44","consensus_level":"high","plddt":87.8539,"start":9,"end":44}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6IEG0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6IEG0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6IEG0-F1-predicted_aligned_error_v6.png","plddt_mean":71.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SNRNP48","jax_strain_url":"https://www.jax.org/strain/search?query=SNRNP48"},"sequence":{"accession":"Q6IEG0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6IEG0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6IEG0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6IEG0"}},"corpus_meta":[{"pmid":"33691721","id":"PMC_33691721","title":"Integrative proteomic and lipidomic analysis of Kaili Sour Soup-mediated attenuation of high-fat diet-induced nonalcoholic fatty liver disease in a rat model.","date":"2021","source":"Nutrition & metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/33691721","citation_count":17,"is_preprint":false},{"pmid":"39809272","id":"PMC_39809272","title":"Structural basis of 5' splice site recognition by the minor spliceosome.","date":"2025","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/39809272","citation_count":7,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3438,"output_tokens":540,"usd":0.009207,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6821,"output_tokens":1160,"usd":0.031552,"stage2_stop_reason":"end_turn"},"total_usd":0.040759,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM reconstruction of the 13-subunit human U11 snRNP complex revealed that SNRNP48 is positioned near the 5' end of U11 snRNA, where it stabilizes binding of the incoming 5' splice site (5'SS). PDCD7 bridges SNRNP25 and SNRNP48, which are located at distal ends of the particle.\",\n      \"method\": \"Cryo-EM structural reconstruction of the human U11 snRNP in apo and substrate-bound forms\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with both apo and substrate-bound states, directly resolving protein positions and interactions within the complex in a single rigorous study\",\n      \"pmids\": [\"39809272\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SNRNP48 and ZMAT5 cooperate to stabilize binding of the incoming U12-type 5' splice site to the U11 snRNP, contributing to 5'SS recognition by the minor spliceosome.\",\n      \"method\": \"Cryo-EM structural analysis of substrate-bound U11 snRNP complex\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct structural visualization of SNRNP48 in substrate-bound conformation, single rigorous study with multiple structural states\",\n      \"pmids\": [\"39809272\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SNRNP48 is a component of the human U11 snRNP complex of the minor spliceosome, where it localizes near the 5' end of U11 snRNA, is bridged to SNRNP25 via PDCD7, and cooperates with ZMAT5 to stabilize recognition of the U12-type 5' splice site through direct structural contacts.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SNRNP48 is a protein component of the human U11 snRNP of the minor spliceosome, where it participates in recognition of U12-type 5' splice sites [#0]. Within the 13-subunit U11 particle, SNRNP48 is positioned near the 5' end of the U11 snRNA and stabilizes binding of the incoming 5' splice site, with PDCD7 bridging SNRNP48 to SNRNP25 across distal ends of the particle [#0]. SNRNP48 acts together with ZMAT5 to stabilize engagement of the U12-type 5' splice site, contributing directly to splice-site recognition by the minor spliceosome [#1]. Beyond its structural role in the U11 snRNP defined by cryo-EM, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"The architecture of the human U11 snRNP and the spatial position of SNRNP48 within it were unknown; resolving the complex established where SNRNP48 sits and how it connects to other subunits.\",\n      \"evidence\": \"Cryo-EM reconstruction of the 13-subunit human U11 snRNP in apo and substrate-bound forms\",\n      \"pmids\": [\"39809272\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Functional consequence of SNRNP48 loss on minor-spliceosome activity not tested\",\n        \"Whether the PDCD7-bridged arrangement is dynamic during the splicing cycle is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"How the minor spliceosome stabilizes the U12-type 5' splice site was unclear; structural analysis showed SNRNP48 and ZMAT5 cooperate to secure this contact.\",\n      \"evidence\": \"Cryo-EM structural analysis of the substrate-bound U11 snRNP\",\n      \"pmids\": [\"39809272\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Quantitative contribution of SNRNP48 versus ZMAT5 to splice-site affinity not separated\",\n        \"No mutational dissection of the residues mediating 5'SS stabilization\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether SNRNP48 has roles beyond the U11 snRNP, and the phenotypic effect of its disruption, remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No loss-of-function or depletion studies in the corpus\",\n        \"No disease association documented\",\n        \"No biochemical activity assigned beyond structural participation\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"U11 snRNP\", \"minor spliceosome\"],\n    \"partners\": [\"PDCD7\", \"SNRNP25\", \"ZMAT5\"],\n    \"other_free_text\": []\n  }\n}\n```","audit_flag":null,"evaluation":{"faith_supported":3,"faith_total":3,"faith_pct":100.0}}