{"gene":"RPL30","run_date":"2026-06-10T07:46:26","timeline":{"discoveries":[{"year":2008,"finding":"Yeast L30 protein binds the nascent RPL30 pre-mRNA at a kink-turn structure including the 5' splice site and blocks splicing by preventing U2 snRNP association with the branch site, without preventing U1 snRNP recognition of the 5' splice site. The branch-point bridging proteins BBP and Mud2 still associate with the intron under L30 repression, indicating L30 acts downstream of initial intron recognition, specifically repressing a spliceosomal rearrangement required for U2 snRNP recruitment.","method":"RNA-protein binding assays, genetic analysis of spliceosomal assembly intermediates, snRNP association assays in yeast","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal biochemical and genetic methods in one study, replicated conceptually by follow-up work (PMID:20801768)","pmids":["18570876"],"is_preprint":false},{"year":2010,"finding":"Using a mutation in the RPL30 binding site that disrupts L30-mediated splicing repression, genetic analysis revealed that deletion of the cap-binding complex component Cbp80 restores splicing repression, demonstrating that Cbp80 plays distinct roles in U1 snRNP recognition of the 5' splice site and in facilitating U2 snRNP recruitment to sequences near the 5' splice site. This places L30-mediated repression downstream of CBC-facilitated U2 recruitment.","method":"Genetic epistasis (deletion of CBP80 in RPL30 binding-site mutant background), splicing assays in yeast","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with functional splicing readout, single lab, two complementary genetic/biochemical approaches","pmids":["20801768"],"is_preprint":false},{"year":1993,"finding":"The promoter of mouse rpL30 contains tandem GABP (GA-binding protein) binding sites in its beta element that can form tetrameric complexes (two alpha + two beta1 subunits) or dimeric complexes with GABP. The proximal site is strongly favored for dimeric complex formation and is more important for promoter function. The potential for tetramer formation from tandem sites has only a minor effect on overall promoter strength.","method":"Electrophoretic mobility shift assay (EMSA) with recombinant GABP subunits and GABP-specific antibodies, footprint analysis, promoter mutant reporter assays","journal":"Gene expression","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — EMSA with recombinant proteins, footprint analysis, and functional promoter mutagenesis, single lab","pmids":["8019128"],"is_preprint":false},{"year":1993,"finding":"Transcription factor RFX1 (a 105-kDa protein) binds the alpha element of the mouse rpL30 promoter and contributes to promoter activity; a mutation in the alpha element abolishing RFX1 interaction reduced rpL30 promoter activity to ~43% of wild-type.","method":"Competition EMSA, antibody supershift assay, promoter mutant reporter assays","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — antibody supershift and functional mutagenesis, single lab, two orthogonal methods","pmids":["8224874"],"is_preprint":false},{"year":1986,"finding":"E. coli ribosomal protein E-L30 adopts a well-defined three-dimensional structure in solution with a triple-stranded beta-sheet, as determined by 2D NMR with near-complete residue-specific resonance assignments (~90% of amino acids assigned) and structural constraints from NOE connectivities.","method":"2D 1H NMR (J-resolved spectroscopy, COSY, DQ spectroscopy, relayed coherence transfer, NOESY) with sequential resonance assignment","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — NMR structure determination with sequential assignments, E. coli ortholog, single lab but two companion papers","pmids":["3550102","3031312"],"is_preprint":false},{"year":1987,"finding":"E. coli ribosomal protein E-L30 undergoes reversible pH-dependent unfolding driven by the degree of protonation of His19 and His33; even when histidines are uncharged the protein has limited stability, attributed to four glutamate residues in its triple-stranded beta-sheet.","method":"500-MHz 1H NMR spectroscopy monitoring folding/unfolding equilibria at varying pH","journal":"Biochemistry","confidence":"Low","confidence_rationale":"Tier 1 / Weak — single NMR study on E. coli ortholog, single lab, no functional consequence established for the unfolding","pmids":["3314990"],"is_preprint":false},{"year":2025,"finding":"In yeast, the importin Kap119/Nmd5 was found in physical proximity to ribosomal protein Rpl30 (eL30) by TurboID-based proximity labeling, suggesting Kap119/Nmd5 interacts with Rpl30 for nuclear import.","method":"TurboID-based proximity labeling (BioID), mass spectrometry","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity labeling only (not direct Co-IP/pulldown), single preprint, no functional validation of the Kap119-Rpl30 interaction reported","pmids":["bio_10.1101_2025.09.18.677003"],"is_preprint":true},{"year":2025,"finding":"Single-molecule FRET using fluorophores introduced into ribosomal proteins uS15 and eL30 was used to monitor intersubunit rotation of yeast (S. cerevisiae) ribosomes; eL30 serves as a FRET donor/acceptor partner to uS15 to report on the nonrotated (NR) vs. rotated (R) conformational states during the elongation cycle. eEF3 was shown to stabilize the NR conformation.","method":"Single-molecule FRET (smFRET) with site-specifically labeled ribosomes, cycloheximide inhibition assay","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — direct smFRET reconstitution with pharmacological and factor-based validation, single preprint lab but multiple orthogonal conditions tested","pmids":["bio_10.1101_2025.06.05.658109"],"is_preprint":true}],"current_model":"RPL30/eL30 is a ribosomal large-subunit protein that autoregulates its own pre-mRNA splicing by binding a kink-turn structure near the 5' splice site of its nascent transcript, blocking a spliceosomal rearrangement required for U2 snRNP recruitment (without preventing U1 snRNP binding); its gene promoter is activated by RFX1 (via the alpha element) and GABP (via tandem beta-element binding sites); the protein has a defined NMR solution structure (triple-stranded beta-sheet, E. coli ortholog); and in yeast it undergoes nuclear import likely via the importin Kap119/Nmd5, while serving as a structural reporter of intersubunit rotation during ribosome translocation."},"narrative":{"mechanistic_narrative":"RPL30/eL30 is a structural protein of the large ribosomal subunit that also functions as a feedback regulator of its own gene expression through control of pre-mRNA splicing [PMID:18570876]. In yeast, L30 binds a kink-turn structure spanning the 5' splice site of its own nascent transcript and represses splicing by blocking U2 snRNP association with the branch site, while leaving U1 snRNP recognition of the 5' splice site and the early branch-point bridging factors BBP and Mud2 intact; this places L30 control at a specific spliceosomal rearrangement required for U2 recruitment rather than at initial intron recognition [PMID:18570876]. Genetic epistasis positions this repression downstream of cap-binding-complex (Cbp80)-facilitated U2 recruitment, since loss of Cbp80 restores repression in a binding-site mutant [PMID:20801768]. Transcription of the gene is driven at its promoter by RFX1 acting through an alpha element and by GABP acting through tandem beta-element sites that form dimeric (favored) or tetrameric complexes [PMID:8019128, PMID:8224874]. The protein has a defined NMR solution structure built around a triple-stranded beta-sheet (E. coli ortholog) [PMID:3550102, PMID:3031312]. Within the assembled ribosome, eL30 reports intersubunit rotation between nonrotated and rotated states during translation elongation [PMID:bio_10.1101_2025.06.05.658109].","teleology":[{"year":1986,"claim":"Establishing the protein's fold answered whether eL30 adopts a discrete, stable tertiary structure, providing the structural baseline for its RNA-binding and ribosomal roles.","evidence":"2D 1H NMR with sequential resonance assignment on the E. coli ortholog","pmids":["3550102","3031312"],"confidence":"Medium","gaps":["Structure is of the E. coli ortholog, not the eukaryotic eL30","Does not address RNA-binding surface or kink-turn recognition","No bound-state or ribosome-context structure"]},{"year":1987,"claim":"Probing folding stability addressed what determines the protein's conformational integrity, identifying histidine protonation and beta-sheet glutamates as destabilizing features.","evidence":"500-MHz 1H NMR monitoring of pH-dependent folding/unfolding equilibria, E. coli ortholog","pmids":["3314990"],"confidence":"Low","gaps":["Single study on E. coli ortholog","No functional consequence established for the unfolding","Relevance to eukaryotic eL30 unknown"]},{"year":1993,"claim":"Dissecting the promoter answered which transcription factors drive RPL30 expression, identifying RFX1 at the alpha element and GABP at tandem beta-element sites.","evidence":"EMSA with recombinant GABP, footprinting, competition/supershift EMSA for RFX1, and promoter mutant reporter assays in mouse","pmids":["8019128","8224874"],"confidence":"Medium","gaps":["Single lab for each factor","Tetramer formation has only minor effect, leaving its physiological role unclear","Does not connect transcriptional control to the splicing autoregulation"]},{"year":2008,"claim":"Mapping where in spliceosome assembly L30 acts answered the long-standing mechanism of its splicing autoregulation, showing it blocks U2 snRNP recruitment downstream of initial intron recognition.","evidence":"RNA-protein binding assays and snRNP/branch-point factor association assays across spliceosomal intermediates in yeast","pmids":["18570876"],"confidence":"High","gaps":["Mechanism of the blocked U2-recruiting rearrangement not structurally resolved","Does not quantify the dynamic range of autoregulation in vivo"]},{"year":2010,"claim":"Genetic epistasis with the cap-binding complex refined the order of events, placing L30 repression downstream of Cbp80-facilitated U2 recruitment.","evidence":"Deletion of CBP80 in an RPL30 binding-site mutant background with splicing readout in yeast","pmids":["20801768"],"confidence":"Medium","gaps":["Single lab","Molecular detail of how Cbp80 facilitates U2 recruitment near the 5' splice site not fully defined"]},{"year":2025,"claim":"Site-specific labeling of eL30 answered whether it can serve as a conformational reporter, establishing it as a FRET partner to uS15 for monitoring intersubunit rotation during elongation.","evidence":"Single-molecule FRET on labeled yeast ribosomes with cycloheximide and eEF3 perturbations (preprint)","pmids":["bio_10.1101_2025.06.05.658109"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Uses eL30 as a structural probe rather than testing an eL30-specific function in rotation","Does not establish a regulatory role for eL30 in translocation"]},{"year":2025,"claim":"Proximity labeling addressed how eL30 reaches the nucleus, placing the importin Kap119/Nmd5 near Rpl30.","evidence":"TurboID proximity labeling and mass spectrometry in yeast (preprint)","pmids":["bio_10.1101_2025.09.18.677003"],"confidence":"Low","gaps":["Proximity labeling only, not direct Co-IP/pulldown","No functional validation of the Kap119-Rpl30 import interaction","Single preprint"]},{"year":null,"claim":"How the transcriptional control of RPL30 and its splicing autoregulation are integrated into a coordinated dosage-control circuit, and whether the eukaryotic eL30 RNA-binding mode is structurally resolved, remains unanswered.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of eukaryotic eL30 bound to the kink-turn","No integration of promoter regulation with splicing feedback","Nuclear import mechanism not functionally validated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[4,7]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1]}],"complexes":["large ribosomal subunit"],"partners":["RFX1","GABP","US15"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P62888","full_name":"Large ribosomal subunit protein eL30","aliases":["60S ribosomal protein L30"],"length_aa":115,"mass_kda":12.8,"function":"Component of the large ribosomal subunit (PubMed:23636399, PubMed:32669547). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:23636399, PubMed:32669547)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P62888/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPL30","classification":"Common Essential","n_dependent_lines":1184,"n_total_lines":1208,"dependency_fraction":0.9801324503311258},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPRIN1","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"RBM8A","stoichiometry":10.0},{"gene":"RPL4","stoichiometry":10.0},{"gene":"RPL5","stoichiometry":10.0},{"gene":"RPS16","stoichiometry":10.0},{"gene":"SRP72","stoichiometry":10.0},{"gene":"DRG1","stoichiometry":4.0},{"gene":"ENY2","stoichiometry":4.0},{"gene":"G3BP2","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/search/RPL30","total_profiled":1310},"omim":[{"mim_id":"601337","title":"REGULATORY FACTOR X, 3; RFX3","url":"https://www.omim.org/entry/601337"},{"mim_id":"600006","title":"REGULATORY FACTOR X, 1; RFX1","url":"https://www.omim.org/entry/600006"},{"mim_id":"180467","title":"RIBOSOMAL PROTEIN L30; RPL30","url":"https://www.omim.org/entry/180467"},{"mim_id":"180466","title":"RIBOSOMAL PROTEIN L19; RPL19","url":"https://www.omim.org/entry/180466"},{"mim_id":"142765","title":"REGULATORY FACTOR X, 2; RFX2","url":"https://www.omim.org/entry/142765"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Endoplasmic reticulum","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPL30"},"hgnc":{"alias_symbol":["L30","eL30"],"prev_symbol":[]},"alphafold":{"accession":"P62888","domains":[{"cath_id":"3.30.1330.30","chopping":"31-100","consensus_level":"medium","plddt":95.1929,"start":31,"end":100}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P62888","model_url":"https://alphafold.ebi.ac.uk/files/AF-P62888-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P62888-F1-predicted_aligned_error_v6.png","plddt_mean":88.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPL30","jax_strain_url":"https://www.jax.org/strain/search?query=RPL30"},"sequence":{"accession":"P62888","fasta_url":"https://rest.uniprot.org/uniprotkb/P62888.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P62888/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P62888"}},"corpus_meta":[{"pmid":"16968546","id":"PMC_16968546","title":"Medulloblastoma outcome is adversely associated with overexpression of EEF1D, RPL30, and RPS20 on the long arm of chromosome 8.","date":"2006","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/16968546","citation_count":62,"is_preprint":false},{"pmid":"1527848","id":"PMC_1527848","title":"A novel oncogene, v-ryk, encoding a truncated receptor tyrosine kinase is transduced into the RPL30 virus without loss of viral sequences.","date":"1992","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/1527848","citation_count":56,"is_preprint":false},{"pmid":"18570876","id":"PMC_18570876","title":"L30 binds the nascent RPL30 transcript to repress U2 snRNP recruitment.","date":"2008","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/18570876","citation_count":49,"is_preprint":false},{"pmid":"8019128","id":"PMC_8019128","title":"Comparative utilization of transcription factor GABP by the promoters of ribosomal protein genes rpL30 and rpL32.","date":"1993","source":"Gene expression","url":"https://pubmed.ncbi.nlm.nih.gov/8019128","citation_count":31,"is_preprint":false},{"pmid":"8224874","id":"PMC_8224874","title":"Transcription factor RFX1 helps control the promoter of the mouse ribosomal protein-encoding gene rpL30 by binding to its alpha element.","date":"1993","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/8224874","citation_count":26,"is_preprint":false},{"pmid":"10343093","id":"PMC_10343093","title":"Integrated genetic and physical map of the 1q31-->q32.1 region, encompassing the RP12 locus, the F13B and HF1 genes, and the EEF1AL11 and RPL30 pseudogenes.","date":"1999","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/10343093","citation_count":19,"is_preprint":false},{"pmid":"3550102","id":"PMC_3550102","title":"Residue-specific assignments of resonances in the 1H nuclear magnetic resonance spectrum of ribosomal protein E-L30 by systematic application of two-dimensional Fourier transform nuclear magnetic resonance methods.","date":"1986","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3550102","citation_count":12,"is_preprint":false},{"pmid":"19922340","id":"PMC_19922340","title":"Rpl30 and Hmgb1 are required for neurulation in golden hamster.","date":"2009","source":"The International journal of neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/19922340","citation_count":10,"is_preprint":false},{"pmid":"20801768","id":"PMC_20801768","title":"RPL30 regulation of splicing reveals distinct roles for Cbp80 in U1 and U2 snRNP cotranscriptional recruitment.","date":"2010","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/20801768","citation_count":10,"is_preprint":false},{"pmid":"3031312","id":"PMC_3031312","title":"Sequential resonance assignments as a basis for the determination of a three-dimensional structure of protein E-L30 of Escherichia coli.","date":"1986","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3031312","citation_count":10,"is_preprint":false},{"pmid":"3314990","id":"PMC_3314990","title":"Reversible unfolding of ribosomal protein E-L30: an NMR study.","date":"1987","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/3314990","citation_count":3,"is_preprint":false},{"pmid":"40495948","id":"PMC_40495948","title":"Anti-RPL30 as a novel biomarker for enhanced diagnosis of autoantibody-negative primary biliary cholangitis.","date":"2025","source":"World journal of gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/40495948","citation_count":2,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.05.658109","title":"Observing intersubunit dynamics in single yeast ribosomes","date":"2025-06-09","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.05.658109","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.09.18.677003","title":"Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1","date":"2025-09-18","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.18.677003","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.26.24315621","title":"5hmC-profiles in Puerto Rican Hispanic/Latino men with aggressive prostate cancer","date":"2024-10-27","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.26.24315621","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9448,"output_tokens":2124,"usd":0.030102,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9054,"output_tokens":2507,"usd":0.053972,"stage2_stop_reason":"end_turn"},"total_usd":0.084074,"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\": 2008,\n      \"finding\": \"Yeast L30 protein binds the nascent RPL30 pre-mRNA at a kink-turn structure including the 5' splice site and blocks splicing by preventing U2 snRNP association with the branch site, without preventing U1 snRNP recognition of the 5' splice site. The branch-point bridging proteins BBP and Mud2 still associate with the intron under L30 repression, indicating L30 acts downstream of initial intron recognition, specifically repressing a spliceosomal rearrangement required for U2 snRNP recruitment.\",\n      \"method\": \"RNA-protein binding assays, genetic analysis of spliceosomal assembly intermediates, snRNP association assays in yeast\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal biochemical and genetic methods in one study, replicated conceptually by follow-up work (PMID:20801768)\",\n      \"pmids\": [\"18570876\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Using a mutation in the RPL30 binding site that disrupts L30-mediated splicing repression, genetic analysis revealed that deletion of the cap-binding complex component Cbp80 restores splicing repression, demonstrating that Cbp80 plays distinct roles in U1 snRNP recognition of the 5' splice site and in facilitating U2 snRNP recruitment to sequences near the 5' splice site. This places L30-mediated repression downstream of CBC-facilitated U2 recruitment.\",\n      \"method\": \"Genetic epistasis (deletion of CBP80 in RPL30 binding-site mutant background), splicing assays in yeast\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with functional splicing readout, single lab, two complementary genetic/biochemical approaches\",\n      \"pmids\": [\"20801768\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"The promoter of mouse rpL30 contains tandem GABP (GA-binding protein) binding sites in its beta element that can form tetrameric complexes (two alpha + two beta1 subunits) or dimeric complexes with GABP. The proximal site is strongly favored for dimeric complex formation and is more important for promoter function. The potential for tetramer formation from tandem sites has only a minor effect on overall promoter strength.\",\n      \"method\": \"Electrophoretic mobility shift assay (EMSA) with recombinant GABP subunits and GABP-specific antibodies, footprint analysis, promoter mutant reporter assays\",\n      \"journal\": \"Gene expression\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — EMSA with recombinant proteins, footprint analysis, and functional promoter mutagenesis, single lab\",\n      \"pmids\": [\"8019128\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Transcription factor RFX1 (a 105-kDa protein) binds the alpha element of the mouse rpL30 promoter and contributes to promoter activity; a mutation in the alpha element abolishing RFX1 interaction reduced rpL30 promoter activity to ~43% of wild-type.\",\n      \"method\": \"Competition EMSA, antibody supershift assay, promoter mutant reporter assays\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — antibody supershift and functional mutagenesis, single lab, two orthogonal methods\",\n      \"pmids\": [\"8224874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1986,\n      \"finding\": \"E. coli ribosomal protein E-L30 adopts a well-defined three-dimensional structure in solution with a triple-stranded beta-sheet, as determined by 2D NMR with near-complete residue-specific resonance assignments (~90% of amino acids assigned) and structural constraints from NOE connectivities.\",\n      \"method\": \"2D 1H NMR (J-resolved spectroscopy, COSY, DQ spectroscopy, relayed coherence transfer, NOESY) with sequential resonance assignment\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure determination with sequential assignments, E. coli ortholog, single lab but two companion papers\",\n      \"pmids\": [\"3550102\", \"3031312\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1987,\n      \"finding\": \"E. coli ribosomal protein E-L30 undergoes reversible pH-dependent unfolding driven by the degree of protonation of His19 and His33; even when histidines are uncharged the protein has limited stability, attributed to four glutamate residues in its triple-stranded beta-sheet.\",\n      \"method\": \"500-MHz 1H NMR spectroscopy monitoring folding/unfolding equilibria at varying pH\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 / Weak — single NMR study on E. coli ortholog, single lab, no functional consequence established for the unfolding\",\n      \"pmids\": [\"3314990\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In yeast, the importin Kap119/Nmd5 was found in physical proximity to ribosomal protein Rpl30 (eL30) by TurboID-based proximity labeling, suggesting Kap119/Nmd5 interacts with Rpl30 for nuclear import.\",\n      \"method\": \"TurboID-based proximity labeling (BioID), mass spectrometry\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity labeling only (not direct Co-IP/pulldown), single preprint, no functional validation of the Kap119-Rpl30 interaction reported\",\n      \"pmids\": [\"bio_10.1101_2025.09.18.677003\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Single-molecule FRET using fluorophores introduced into ribosomal proteins uS15 and eL30 was used to monitor intersubunit rotation of yeast (S. cerevisiae) ribosomes; eL30 serves as a FRET donor/acceptor partner to uS15 to report on the nonrotated (NR) vs. rotated (R) conformational states during the elongation cycle. eEF3 was shown to stabilize the NR conformation.\",\n      \"method\": \"Single-molecule FRET (smFRET) with site-specifically labeled ribosomes, cycloheximide inhibition assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct smFRET reconstitution with pharmacological and factor-based validation, single preprint lab but multiple orthogonal conditions tested\",\n      \"pmids\": [\"bio_10.1101_2025.06.05.658109\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"RPL30/eL30 is a ribosomal large-subunit protein that autoregulates its own pre-mRNA splicing by binding a kink-turn structure near the 5' splice site of its nascent transcript, blocking a spliceosomal rearrangement required for U2 snRNP recruitment (without preventing U1 snRNP binding); its gene promoter is activated by RFX1 (via the alpha element) and GABP (via tandem beta-element binding sites); the protein has a defined NMR solution structure (triple-stranded beta-sheet, E. coli ortholog); and in yeast it undergoes nuclear import likely via the importin Kap119/Nmd5, while serving as a structural reporter of intersubunit rotation during ribosome translocation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL30/eL30 is a structural protein of the large ribosomal subunit that also functions as a feedback regulator of its own gene expression through control of pre-mRNA splicing [#0]. In yeast, L30 binds a kink-turn structure spanning the 5' splice site of its own nascent transcript and represses splicing by blocking U2 snRNP association with the branch site, while leaving U1 snRNP recognition of the 5' splice site and the early branch-point bridging factors BBP and Mud2 intact; this places L30 control at a specific spliceosomal rearrangement required for U2 recruitment rather than at initial intron recognition [#0]. Genetic epistasis positions this repression downstream of cap-binding-complex (Cbp80)-facilitated U2 recruitment, since loss of Cbp80 restores repression in a binding-site mutant [#1]. Transcription of the gene is driven at its promoter by RFX1 acting through an alpha element and by GABP acting through tandem beta-element sites that form dimeric (favored) or tetrameric complexes [#2, #3]. The protein has a defined NMR solution structure built around a triple-stranded beta-sheet (E. coli ortholog) [#4]. Within the assembled ribosome, eL30 reports intersubunit rotation between nonrotated and rotated states during translation elongation [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 1986,\n      \"claim\": \"Establishing the protein's fold answered whether eL30 adopts a discrete, stable tertiary structure, providing the structural baseline for its RNA-binding and ribosomal roles.\",\n      \"evidence\": \"2D 1H NMR with sequential resonance assignment on the E. coli ortholog\",\n      \"pmids\": [\"3550102\", \"3031312\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structure is of the E. coli ortholog, not the eukaryotic eL30\", \"Does not address RNA-binding surface or kink-turn recognition\", \"No bound-state or ribosome-context structure\"]\n    },\n    {\n      \"year\": 1987,\n      \"claim\": \"Probing folding stability addressed what determines the protein's conformational integrity, identifying histidine protonation and beta-sheet glutamates as destabilizing features.\",\n      \"evidence\": \"500-MHz 1H NMR monitoring of pH-dependent folding/unfolding equilibria, E. coli ortholog\",\n      \"pmids\": [\"3314990\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single study on E. coli ortholog\", \"No functional consequence established for the unfolding\", \"Relevance to eukaryotic eL30 unknown\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Dissecting the promoter answered which transcription factors drive RPL30 expression, identifying RFX1 at the alpha element and GABP at tandem beta-element sites.\",\n      \"evidence\": \"EMSA with recombinant GABP, footprinting, competition/supershift EMSA for RFX1, and promoter mutant reporter assays in mouse\",\n      \"pmids\": [\"8019128\", \"8224874\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab for each factor\", \"Tetramer formation has only minor effect, leaving its physiological role unclear\", \"Does not connect transcriptional control to the splicing autoregulation\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Mapping where in spliceosome assembly L30 acts answered the long-standing mechanism of its splicing autoregulation, showing it blocks U2 snRNP recruitment downstream of initial intron recognition.\",\n      \"evidence\": \"RNA-protein binding assays and snRNP/branch-point factor association assays across spliceosomal intermediates in yeast\",\n      \"pmids\": [\"18570876\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of the blocked U2-recruiting rearrangement not structurally resolved\", \"Does not quantify the dynamic range of autoregulation in vivo\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Genetic epistasis with the cap-binding complex refined the order of events, placing L30 repression downstream of Cbp80-facilitated U2 recruitment.\",\n      \"evidence\": \"Deletion of CBP80 in an RPL30 binding-site mutant background with splicing readout in yeast\",\n      \"pmids\": [\"20801768\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Molecular detail of how Cbp80 facilitates U2 recruitment near the 5' splice site not fully defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Site-specific labeling of eL30 answered whether it can serve as a conformational reporter, establishing it as a FRET partner to uS15 for monitoring intersubunit rotation during elongation.\",\n      \"evidence\": \"Single-molecule FRET on labeled yeast ribosomes with cycloheximide and eEF3 perturbations (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.06.05.658109\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Uses eL30 as a structural probe rather than testing an eL30-specific function in rotation\", \"Does not establish a regulatory role for eL30 in translocation\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Proximity labeling addressed how eL30 reaches the nucleus, placing the importin Kap119/Nmd5 near Rpl30.\",\n      \"evidence\": \"TurboID proximity labeling and mass spectrometry in yeast (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.09.18.677003\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Proximity labeling only, not direct Co-IP/pulldown\", \"No functional validation of the Kap119-Rpl30 import interaction\", \"Single preprint\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the transcriptional control of RPL30 and its splicing autoregulation are integrated into a coordinated dosage-control circuit, and whether the eukaryotic eL30 RNA-binding mode is structurally resolved, remains unanswered.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of eukaryotic eL30 bound to the kink-turn\", \"No integration of promoter regulation with splicing feedback\", \"Nuclear import mechanism not functionally validated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [4, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"large ribosomal subunit\"],\n    \"partners\": [\"RFX1\", \"GABP\", \"uS15\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":5,"faith_pct":80.0}}