{"gene":"TMA16","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2020,"finding":"TMA16 is localized between the 5S RNA and the P0 stalk in human pre-60S ribosomal particles, as determined by cryo-EM structural snapshots of particles isolated through the nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export.","method":"Cryo-EM structural analysis of human pre-60S ribosomal particles isolated via NMD3","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with defined localization of TMA16 within the pre-60S particle, single lab but high-resolution structural method with multiple particle snapshots","pmids":["32669547"],"is_preprint":false}],"current_model":"TMA16 is a pre-60S ribosome assembly factor that localizes between the 5S RNA and the P0 stalk in human pre-60S ribosomal particles at assembly stages immediately before and after nuclear export."},"narrative":{"mechanistic_narrative":"TMA16 is a factor associated with the human pre-60S ribosomal particle, positioned between the 5S RNA and the P0 stalk during the late nuclear maturation steps of large ribosomal subunit assembly [PMID:32669547]. Cryo-EM analysis of pre-60S particles isolated through the nuclear export factor NMD3 places TMA16 at this site in assembly intermediates captured immediately before and after nuclear export, linking it to the stages of 60S maturation that bridge the nucleus and cytoplasm [PMID:32669547]. Beyond this structural localization [PMID:32669547], no further mechanistic detail, biochemical activity, or interaction network for TMA16 has been characterized in the available corpus.","teleology":[{"year":2020,"claim":"Whether TMA16 participates in human ribosome biogenesis and where it acts on the maturing subunit was unknown; visualizing it within export-stage pre-60S particles established it as a late large-subunit assembly factor positioned at the 5S RNA/P0 stalk interface.","evidence":"Cryo-EM structural analysis of human pre-60S ribosomal particles isolated via the nuclear export factor NMD3","pmids":["32669547"],"confidence":"High","gaps":["No biochemical activity or function assigned to TMA16 within the particle","Mechanism of recruitment and release relative to nuclear export is not defined","Effect of TMA16 depletion on 60S maturation or cell growth not tested"]},{"year":null,"claim":"It remains unknown what molecular activity TMA16 contributes to pre-60S maturation and how its association is coordinated with the 5S RNP and stalk assembly.","evidence":"","pmids":[],"confidence":"High","gaps":["No functional or loss-of-function characterization in the available corpus","No defined binding partners beyond structural proximity to 5S RNA and P0 stalk"]}],"mechanism_profile":{"molecular_activity":[],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0]}],"complexes":["pre-60S ribosomal particle"],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96EY4","full_name":"Translation machinery-associated protein 16","aliases":[],"length_aa":203,"mass_kda":23.9,"function":"Involved in the biogenesis of the 60S ribosomal subunit in the nucleus","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q96EY4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/TMA16","classification":"Common Essential","n_dependent_lines":1132,"n_total_lines":1208,"dependency_fraction":0.9370860927152318},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000198498","cell_line_id":"CID001090","localizations":[{"compartment":"nucleolus_gc","grade":3},{"compartment":"nucleoplasm","grade":1}],"interactors":[{"gene":"RPS6KB2","stoichiometry":10.0},{"gene":"TNPO1","stoichiometry":10.0},{"gene":"MRPS15","stoichiometry":0.2},{"gene":"HK2","stoichiometry":0.2},{"gene":"TNPO2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001090","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli","reliability":"Enhanced"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMA16"},"hgnc":{"alias_symbol":["FLJ11184"],"prev_symbol":["C4orf43"]},"alphafold":{"accession":"Q96EY4","domains":[{"cath_id":"1.20.1440.170","chopping":"23-167","consensus_level":"high","plddt":91.855,"start":23,"end":167}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96EY4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96EY4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96EY4-F1-predicted_aligned_error_v6.png","plddt_mean":82.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMA16","jax_strain_url":"https://www.jax.org/strain/search?query=TMA16"},"sequence":{"accession":"Q96EY4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96EY4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96EY4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96EY4"}},"corpus_meta":[{"pmid":"32669547","id":"PMC_32669547","title":"Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32669547","citation_count":64,"is_preprint":false},{"pmid":"28916784","id":"PMC_28916784","title":"P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28916784","citation_count":33,"is_preprint":false},{"pmid":"26865924","id":"PMC_26865924","title":"Genome-wide association study for the interaction between BMR and BMI in obese Korean women including overweight.","date":"2015","source":"Nutrition research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/26865924","citation_count":24,"is_preprint":false},{"pmid":"40527220","id":"PMC_40527220","title":"Characterization of methylation profile in biofluid cell-free DNA and identification of differentially methylated genes for phenotypic representations in Parkinson's disease.","date":"2025","source":"Clinical neurology and neurosurgery","url":"https://pubmed.ncbi.nlm.nih.gov/40527220","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4293,"output_tokens":291,"usd":0.008622,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6491,"output_tokens":888,"usd":0.027328,"stage2_stop_reason":"end_turn"},"total_usd":0.03595,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"TMA16 is localized between the 5S RNA and the P0 stalk in human pre-60S ribosomal particles, as determined by cryo-EM structural snapshots of particles isolated through the nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export.\",\n      \"method\": \"Cryo-EM structural analysis of human pre-60S ribosomal particles isolated via NMD3\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with defined localization of TMA16 within the pre-60S particle, single lab but high-resolution structural method with multiple particle snapshots\",\n      \"pmids\": [\"32669547\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TMA16 is a pre-60S ribosome assembly factor that localizes between the 5S RNA and the P0 stalk in human pre-60S ribosomal particles at assembly stages immediately before and after nuclear export.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TMA16 is a factor associated with the human pre-60S ribosomal particle, positioned between the 5S RNA and the P0 stalk during the late nuclear maturation steps of large ribosomal subunit assembly [#0]. Cryo-EM analysis of pre-60S particles isolated through the nuclear export factor NMD3 places TMA16 at this site in assembly intermediates captured immediately before and after nuclear export, linking it to the stages of 60S maturation that bridge the nucleus and cytoplasm [#0]. Beyond this structural localization [#0], no further mechanistic detail, biochemical activity, or interaction network for TMA16 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether TMA16 participates in human ribosome biogenesis and where it acts on the maturing subunit was unknown; visualizing it within export-stage pre-60S particles established it as a late large-subunit assembly factor positioned at the 5S RNA/P0 stalk interface.\",\n      \"evidence\": \"Cryo-EM structural analysis of human pre-60S ribosomal particles isolated via the nuclear export factor NMD3\",\n      \"pmids\": [\n        \"32669547\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No biochemical activity or function assigned to TMA16 within the particle\",\n        \"Mechanism of recruitment and release relative to nuclear export is not defined\",\n        \"Effect of TMA16 depletion on 60S maturation or cell growth not tested\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown what molecular activity TMA16 contributes to pre-60S maturation and how its association is coordinated with the 5S RNP and stalk assembly.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No functional or loss-of-function characterization in the available corpus\",\n        \"No defined binding partners beyond structural proximity to 5S RNA and P0 stalk\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"pre-60S ribosomal particle\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":2,"faith_total":2,"faith_pct":100.0}}