{"gene":"RPS13","run_date":"2026-06-10T07:46:27","timeline":{"discoveries":[{"year":2007,"finding":"Human RPS13 specifically binds to a fragment of its own pre-mRNA encompassing exons 1 and 2, intron 1, and part of intron 2, and inhibits splicing of intron 1 in vitro, providing ribonuclease protection at sequences near the 5' and 3' splice sites; this constitutes a feedback autoregulatory mechanism controlling RPS13 expression at the splicing step.","method":"In vitro splicing inhibition assay with recombinant rpS13; RNase protection mapping of protein-binding sites on pre-mRNA; transfection of HEK 293 cells with minigene containing intron 1","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal methods (in vitro binding, RNase protection, cell-based minigene assay) in single study; specificity confirmed with rpS10 and rpS16 controls","pmids":["17881366","17380891"],"is_preprint":false},{"year":2004,"finding":"Overexpression of human RPS13 in gastric cancer cells (SGC7901) promotes multidrug resistance by suppressing drug-induced apoptosis and significantly increasing Bcl-2 expression and Bcl-2/Bax ratio, without altering drug accumulation or protein synthesis rates.","method":"Genetic overexpression of RPS13 in gastric cancer cells; cell viability and apoptosis assays; Western blot for Bcl-2/Bax; [3H]leucine incorporation; intracellular drug accumulation measurement","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — multiple functional assays in single lab, gain-of-function with defined molecular readout (Bcl-2/Bax ratio)","pmids":["15149863"],"is_preprint":false},{"year":2011,"finding":"RPS13 promotes gastric cancer cell growth and G1-to-S phase transition by down-regulating p27(Kip1) expression and reducing CDK2 kinase activity, without altering cyclin D, cyclin E, CDK2, CDK4, or p16(INK4A) levels.","method":"RPS13 overexpression and RNAi knockdown in gastric cancer cells; cell cycle analysis by flow cytometry; Western blot for cell cycle regulators; CDK2 kinase activity assay; in vivo tumor formation assay","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal gain- and loss-of-function with multiple orthogonal readouts in single lab","pmids":["19912438"],"is_preprint":false},{"year":2005,"finding":"E. coli ribosomal protein S13 (bacterial ortholog of RPS13/uS15) is required for ribosome subunit association, translation initiation, and translocation; targeted mutagenesis of S13 bridge contact elements and tRNA contact elements (C-terminal extension) each individually impair translational fidelity and efficiency, indicating S13 provides signal transduction between the tRNA-binding site and the small subunit head during translocation.","method":"rpsM(S13)-deficient E. coli strain; in vitro subunit association, initiation, and translocation assays; targeted mutagenesis of bridge and tRNA contact residues","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution assays combined with targeted mutagenesis, multiple functional readouts in single rigorous study","pmids":["15876367"],"is_preprint":false},{"year":2004,"finding":"In the 30S ribosomal subunit assembly map, S13 (bacterial ortholog) requires prior association of S7 (not S20 as previously mapped) for binding to the 16S rRNA ribonucleoprotein particle, placing S13 in the S7 assembly branch consistent with its head location; S13 also makes cooperative interactions with other S7-branch proteins.","method":"Base-specific chemical footprinting; primer extension analysis; single protein addition and omission studies","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple footprinting approaches in single lab correcting prior assembly map placement","pmids":["15525707"],"is_preprint":false},{"year":1988,"finding":"E. coli ribosomal protein S13 (bacterial ortholog) is cross-linked to proteins S19 in the 30S subunit, with the cross-link site identified at Cys84 of S13 and His68 of S19 by diepoxybutane cross-linking followed by peptide sequencing, FAB-MS, and amino acid analysis.","method":"Bifunctional cross-linker diepoxybutane treatment of 30S subunits; HPLC purification of cross-linked S13–S19 complex; enzymatic fragmentation; sequence analysis; FAB-MS","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-level identification of cross-link site by peptide sequencing and MS, replicated in Bacillus stearothermophilus (PMID 3291949)","pmids":["3279034","3291949"],"is_preprint":false},{"year":1985,"finding":"E. coli ribosomal protein S13 has two separable functional domains: a C-terminal fragment (residues 84–117) retains 16S rRNA-binding activity at multiple sites, while the N-terminal region is important for association with protein S19, as demonstrated by proteolytic cleavage and filter-binding assays.","method":"Proteolytic cleavage of S13 into two polypeptides; nitrocellulose filter-binding assay for RNA binding; S19 competition binding assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain dissection with in vitro binding assays, single lab","pmids":["3903659"],"is_preprint":false},{"year":1996,"finding":"Directed hydroxyl radical probing from Fe(II) tethered to Cys84 of E. coli S13 (bacterial ortholog) in reconstituted 30S subunits localizes S13 adjacent to two regions of 16S rRNA: nucleotides 1308–1333 in the 3' major domain and the 950/1230 helix.","method":"In vitro reconstitution of 30S subunits with Fe(II)-EDTA derivatized S13; hydroxyl radical cleavage mapping of 16S rRNA","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — site-specific tethered cleavage in reconstituted subunit, rigorous localization of protein–RNA contacts","pmids":["8718688"],"is_preprint":false},{"year":1987,"finding":"E. coli ribosomal protein S13 (bacterial ortholog) is cross-linked to 16S rRNA at oligonucleotide positions 1337–1338 and anomalously at positions 189–191 in the 30S subunit, using methyl p-azidophenyl acetimidate photo-cross-linking.","method":"Photo-cross-linking with methyl p-azidophenyl acetimidate; partial nuclease digestion; isolation of RNA–protein complexes; RNA and protein analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct RNA–protein cross-linking with site identification, single study","pmids":["2437527"],"is_preprint":false},{"year":1988,"finding":"Ribosomal proteins S2, S3, S10, S13, and S14 bind to the 3' major domain of 16S rRNA; S13 and S14 each protect distinct nucleotides adjacent to regions previously protected by S19, as revealed by chemical and enzymatic probing during assembly of the 30S subunit.","method":"Chemical and enzymatic probing of 16S rRNA during stepwise assembly; monospecific and cooperative protection pattern analysis","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic probing during assembly, multiple proteins and conditions, single lab","pmids":["2459390"],"is_preprint":false},{"year":1981,"finding":"Rat liver ribosomal protein S13 specifically binds to 5.8S rRNA with a single binding site per RNA molecule and an apparent association constant in the range of 0.2–18 × 10^5 M^-1 (measured at 4°C and 22°C), as determined by nitrocellulose membrane filtration.","method":"Nitrocellulose membrane filter binding assay with purified rat liver rpS13 and 5.8S rRNA; saturation binding and stoichiometry analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct binding assay with defined stoichiometry, single lab, single method","pmids":["7251593"],"is_preprint":false},{"year":1994,"finding":"A C-terminal truncation of E. coli S13 (rpsM mutation removing 19 C-terminal amino acids, including the RNA-binding C-terminal domain) causes decreased translational step time, reduced growth rate, and strong antisuppression of amber and opal suppressors, consistent with impaired ribosomal function; the truncated small subunit shows reduced sedimentation but forms apparently normal 70S ribosomes.","method":"Cloning and sequencing of rpsM mutation; sucrose gradient ultracentrifugation; suppressor activity assays in vivo","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical characterization of defined loss-of-function allele, multiple phenotypic readouts","pmids":["8193163"],"is_preprint":false},{"year":2020,"finding":"Drosophila RpS13 is required for germline stem cell self-renewal and differentiation in the testis niche; knockdown of RpS13 affects cell proliferation and apoptosis and modulates expression of ribosome subunits, Rho1, DE-cad (E-cadherin), and Armadillo (β-catenin); Rho1 overexpression phenocopies RpS13 loss, placing RpS13 upstream of Rho1-mediated cell adhesion signaling.","method":"Tissue-specific RNAi knockdown in Drosophila testes and S2 cells; immunofluorescence for stem cell markers; TUNEL/flow cytometry for apoptosis; qRT-PCR; genetic epistasis with Rho1","journal":"Cell proliferation","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — genetic epistasis with multiple readouts, single lab, Drosophila ortholog","pmids":["32896929"],"is_preprint":false},{"year":1996,"finding":"Loss-of-function P-element insertion in Drosophila RpS13 (encoding the Drosophila ortholog of ribosomal protein S13) causes the Minute phenotype (short thin bristles, slow development) and reduces RPS13 transcript to ~50%; the phenotype is rescued by P-element remobilization, establishing this as a classical Minute ribosomal protein gene.","method":"P-element mutagenesis; sequencing of interrupted gene; Northern blot quantification of transcript; genetic rescue by P-element excision","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct insertion mutagenesis with genetic rescue, single lab","pmids":["8725235"],"is_preprint":false},{"year":1993,"finding":"Protein S13 (DNP-labeled) in reconstituted E. coli 30S subunits is localized by immune electron microscopy to the subunit head above the platform and on the surface facing the large subunit, confirming its position at the subunit interface.","method":"Dinitrophenylation of S13; total reconstitution of 30S subunits with DNP-S13; immune electron microscopy with anti-DNP antibodies","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct structural localization by immune EM in reconstituted particles, single lab","pmids":["8360163"],"is_preprint":false},{"year":2013,"finding":"Mg2+ ions (at concentrations 0.5–20 mM) reduce the affinity of human rpS13 for the central domain fragment of 18S rRNA by inducing structural rearrangements in helices H20 and H22 of the 18S rRNA central domain that mimic the conformation found in assembled 40S subunits, as detected by hydroxyl radical probing.","method":"In vitro binding of recombinant human rpS13 to 18S rRNA central domain RNA; hydroxyl radical probing of RNA structure at varying Mg2+ concentrations","journal":"Molekuliarnaia biologiia","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single biochemical method, single lab, limited mechanistic follow-up","pmids":["23705505"],"is_preprint":false},{"year":1996,"finding":"U14 small nucleolar RNAs (snoRNAs) are encoded within introns 3 and 5 of the human RPS13 gene, identified by PCR cloning and sequencing of the intron-containing genomic locus; the gene structure comprises 6 exons and 5 introns spanning 3.3 kb.","method":"PCR cloning and sequencing of intron-containing human S13 genomic gene; sequence comparison with Xenopus U14 snoRNA genes","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct genomic sequencing establishing structural organization, replicated feature across species","pmids":["8920921"],"is_preprint":false}],"current_model":"RPS13 (uS15) is a conserved small ribosomal subunit protein that occupies the head region of the 40S/30S subunit, contacts 16S/18S rRNA in the 3' major domain and 5.8S rRNA, bridges the inter-subunit interface through interactions with the large subunit and P-site tRNA via its C-terminal extension, and is required for subunit association, translation initiation, and translocation fidelity; in addition, free RPS13 protein feeds back to inhibit splicing of its own pre-mRNA at intron 1 as an autoregulatory mechanism, and in cancer cells elevated RPS13 suppresses apoptosis by upregulating Bcl-2/Bax and promotes cell cycle progression by down-regulating p27(Kip1)."},"narrative":{"mechanistic_narrative":"RPS13 (uS15) is a conserved small ribosomal subunit protein of the 40S/30S head whose direct RNA contacts and inter-subunit position underpin core steps of translation [PMID:15876367, PMID:8718688]. It binds the 3' major domain of 16S/18S rRNA (contacting nucleotides ~1308–1338 and the 950/1230 helix) through its C-terminal RNA-binding domain, while the eukaryotic protein also binds 5.8S rRNA, establishing it as a multivalent rRNA-binding protein within the subunit head [PMID:8718688, PMID:2437527, PMID:7251593, PMID:3903659]. During 30S assembly it joins via the S7 branch and makes cooperative contacts with neighboring head proteins, including a defined cross-link to S19 mediated by its N-terminal region [PMID:15525707, PMID:2459390, PMID:3279034, PMID:3291949, PMID:3903659]. Functionally, RPS13 is required for subunit association, translation initiation, and translocation: its bridge contacts and tRNA-contacting C-terminal extension transmit signals between the tRNA-binding site and the subunit head, and truncation of the C-terminus impairs translational step time and fidelity [PMID:15876367, PMID:8193163, PMID:8360163]. Beyond the ribosome, free RPS13 protein binds its own pre-mRNA and inhibits splicing of intron 1, constituting a feedback autoregulatory loop controlling its expression [PMID:17881366, PMID:17380891]. In Drosophila the gene behaves as a classical Minute locus required for normal growth and for germline stem cell self-renewal, acting upstream of Rho1-mediated adhesion signaling [PMID:8725235, PMID:32896929]. In gastric cancer cells, elevated RPS13 suppresses drug-induced apoptosis by raising the Bcl-2/Bax ratio and drives G1-to-S progression by down-regulating p27(Kip1) and reducing CDK2 activity [PMID:15149863, PMID:19912438].","teleology":[{"year":1981,"claim":"Established that the eukaryotic protein has intrinsic rRNA-binding specificity by showing direct, stoichiometric binding to 5.8S rRNA, distinguishing it from purely bacterial-defined contacts.","evidence":"Nitrocellulose filter binding of purified rat liver rpS13 to 5.8S rRNA with stoichiometry analysis","pmids":["7251593"],"confidence":"Medium","gaps":["Binding site on 5.8S rRNA not mapped at nucleotide resolution","Functional consequence within assembled 60S/80S not addressed"]},{"year":1985,"claim":"Resolved the domain architecture of the protein, showing RNA binding and inter-protein contact map to separable regions.","evidence":"Proteolytic dissection of E. coli S13 with filter-binding and S19 competition assays","pmids":["3903659"],"confidence":"Medium","gaps":["Residue-level boundaries of the two functions not defined","Bacterial ortholog; eukaryotic domain map inferred"]},{"year":1987,"claim":"Mapped direct protein–rRNA cross-link sites, anchoring S13 to specific 16S rRNA positions.","evidence":"Photo-cross-linking with methyl p-azidophenyl acetimidate and nuclease mapping in 30S subunits","pmids":["2437527"],"confidence":"Medium","gaps":["Anomalous 189–191 cross-link unexplained","Single cross-linking chemistry"]},{"year":1988,"claim":"Defined the head-region neighbor of S13 by identifying its protein partner and the precise cross-link residues, and placed it among 3' major domain binders.","evidence":"Diepoxybutane cross-linking with peptide sequencing/FAB-MS (S13–S19), plus assembly probing of the 3' major domain","pmids":["3279034","3291949","2459390"],"confidence":"High","gaps":["Functional significance of the S13–S19 contact not tested","Eukaryotic equivalence of partner contact not shown"]},{"year":1994,"claim":"Linked the C-terminal RNA-binding domain to translational performance by phenotyping a defined truncation allele.","evidence":"rpsM C-terminal truncation in E. coli; sucrose gradients and suppressor activity assays","pmids":["8193163"],"confidence":"Medium","gaps":["Molecular step defect not isolated in vitro","Effect on initiation versus elongation not separated"]},{"year":1996,"claim":"Localized the protein within the 16S rRNA tertiary fold and within the subunit by tethered cleavage and immune EM, and revealed that the gene host encodes intronic U14 snoRNAs.","evidence":"Fe(II)-tethered hydroxyl radical probing from Cys84; immune EM of reconstituted 30S; genomic sequencing of the human S13 locus","pmids":["8718688","8360163","8920921"],"confidence":"High","gaps":["Whether U14 processing depends on RPS13 transcription/splicing not tested","Interface position confirmed structurally but functional bridging assayed later"]},{"year":1996,"claim":"Established the gene as a haploinsufficient growth determinant, the classical Minute phenotype, by mutagenesis and genetic rescue.","evidence":"P-element insertion in Drosophila RpS13 with Northern quantification and rescue by excision","pmids":["8725235"],"confidence":"Medium","gaps":["Mechanism linking reduced ribosomal protein to bristle/growth phenotype not dissected","Drosophila ortholog"]},{"year":2004,"claim":"Refined the 30S assembly pathway, reassigning S13 dependency from S20 to S7 and showing cooperative head-protein interactions.","evidence":"Chemical footprinting and single-protein addition/omission assembly studies","pmids":["15525707"],"confidence":"Medium","gaps":["Kinetics of assembly not measured","Eukaryotic assembly order not addressed"]},{"year":2004,"claim":"Connected RPS13 dosage to cancer cell survival, showing overexpression confers multidrug resistance via apoptosis suppression independent of translation rate.","evidence":"RPS13 overexpression in SGC7901 gastric cancer cells; apoptosis assays, Bcl-2/Bax Western, drug accumulation and [3H]leucine incorporation","pmids":["15149863"],"confidence":"Medium","gaps":["Direct molecular link between RPS13 and Bcl-2 regulation unknown","Single cell line"]},{"year":2005,"claim":"Defined the core ribosomal mechanism of the protein, demonstrating it transmits signals between the tRNA site and subunit head during translocation through distinct bridge and tRNA-contact elements.","evidence":"rpsM-deficient E. coli with in vitro association/initiation/translocation assays and targeted mutagenesis","pmids":["15876367"],"confidence":"High","gaps":["Real-time conformational coupling not visualized","Eukaryotic translocation role inferred from bacterial ortholog"]},{"year":2007,"claim":"Revealed a non-ribosomal autoregulatory function, showing free RPS13 protein binds its own pre-mRNA and inhibits intron 1 splicing.","evidence":"In vitro splicing inhibition, RNase protection mapping, and minigene assays in HEK293 with rpS10/rpS16 specificity controls","pmids":["17881366","17380891"],"confidence":"High","gaps":["Cellular threshold of free RPS13 triggering autoregulation not quantified","Spliceosomal factors involved not identified"]},{"year":2011,"claim":"Extended the oncogenic role to cell cycle control, showing RPS13 drives G1/S transition via p27(Kip1) down-regulation and reduced CDK2 activity.","evidence":"Reciprocal overexpression/knockdown in gastric cancer cells; flow cytometry, Western blots, CDK2 kinase assay, in vivo tumor formation","pmids":["19912438"],"confidence":"Medium","gaps":["Mechanism of p27 regulation by RPS13 unresolved","Whether effect is ribosome-dependent not addressed"]},{"year":2013,"claim":"Probed how rRNA conformation gates RPS13 binding, showing Mg2+-induced 18S rearrangements lower its affinity.","evidence":"In vitro binding of recombinant human rpS13 to 18S central domain with hydroxyl radical probing at varying Mg2+","pmids":["23705505"],"confidence":"Low","gaps":["Single biochemical method without independent confirmation","Physiological relevance during assembly not established"]},{"year":2020,"claim":"Placed RPS13 in a developmental signaling context, showing it controls germline stem cell self-renewal upstream of Rho1-mediated adhesion.","evidence":"Tissue-specific RNAi in Drosophila testes/S2 cells with stem cell markers, apoptosis assays, qRT-PCR, and Rho1 epistasis","pmids":["32896929"],"confidence":"Medium","gaps":["Whether the role is extraribosomal or via translation not separated","Direct link to Rho1/cadherin pathway not biochemically defined"]},{"year":null,"claim":"It remains unresolved whether the cancer-associated apoptosis and cell-cycle phenotypes and the Drosophila adhesion role reflect extraribosomal moonlighting functions of RPS13 or downstream consequences of altered ribosome biogenesis/translation.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct molecular targets identified for the apoptosis/cell-cycle effects","Extraribosomal versus ribosomal contributions not separated","No human structural model of RPS13 within 40S in this corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[7,8,10,6,0]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[3,14]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[3,11]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[3,14,7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0]}],"complexes":["40S/30S small ribosomal subunit"],"partners":["RPS19"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P62277","full_name":"Small ribosomal subunit protein uS15","aliases":["40S ribosomal protein S13"],"length_aa":151,"mass_kda":17.2,"function":"Component of the small ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome (PubMed:34516797)","subcellular_location":"Cytoplasm; Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/P62277/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPS13","classification":"Common Essential","n_dependent_lines":1205,"n_total_lines":1208,"dependency_fraction":0.9975165562913907},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DRG1","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"EIF3B","stoichiometry":10.0},{"gene":"RACK1","stoichiometry":10.0},{"gene":"RBM8A","stoichiometry":10.0},{"gene":"RPL11","stoichiometry":10.0},{"gene":"RPL5","stoichiometry":10.0},{"gene":"RPS16","stoichiometry":10.0},{"gene":"SRP72","stoichiometry":10.0},{"gene":"SRP9","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/RPS13","total_profiled":1310},"omim":[{"mim_id":"608610","title":"PROGRAMMED CELL DEATH 4; PDCD4","url":"https://www.omim.org/entry/608610"},{"mim_id":"180476","title":"RIBOSOMAL PROTEIN S13; RPS13","url":"https://www.omim.org/entry/180476"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Endoplasmic reticulum","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPS13"},"hgnc":{"alias_symbol":["S13","uS15"],"prev_symbol":[]},"alphafold":{"accession":"P62277","domains":[{"cath_id":"1.10.287.10","chopping":"85-148","consensus_level":"high","plddt":94.8598,"start":85,"end":148},{"cath_id":"1.10.10","chopping":"29-77","consensus_level":"high","plddt":95.5141,"start":29,"end":77}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P62277","model_url":"https://alphafold.ebi.ac.uk/files/AF-P62277-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P62277-F1-predicted_aligned_error_v6.png","plddt_mean":94.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPS13","jax_strain_url":"https://www.jax.org/strain/search?query=RPS13"},"sequence":{"accession":"P62277","fasta_url":"https://rest.uniprot.org/uniprotkb/P62277.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P62277/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P62277"}},"corpus_meta":[{"pmid":"8709095","id":"PMC_8709095","title":"(S)-13-[(dimethylamino)methyl]-10,11,14,15-tetrahydro-4,9:16, 21-dimetheno-1H, 13H-dibenzo[e,k]pyrrolo[3,4-h][1,4,13]oxadiazacyclohexadecene-1,3(2H)-d ione (LY333531) and related analogues: isozyme selective inhibitors of protein kinase C beta.","date":"1996","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8709095","citation_count":277,"is_preprint":false},{"pmid":"15149863","id":"PMC_15149863","title":"Ribosomal proteins S13 and L23 promote multidrug resistance in gastric cancer cells by suppressing drug-induced apoptosis.","date":"2004","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/15149863","citation_count":97,"is_preprint":false},{"pmid":"15651040","id":"PMC_15651040","title":"Structure and biosynthesis of myxochromides S1-3 in Stigmatella aurantiaca: evidence for an iterative bacterial type I polyketide synthase and for module skipping in nonribosomal peptide biosynthesis.","date":"2005","source":"Chembiochem : a European journal of chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/15651040","citation_count":89,"is_preprint":false},{"pmid":"3288761","id":"PMC_3288761","title":"Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli.","date":"1988","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3288761","citation_count":88,"is_preprint":false},{"pmid":"947902","id":"PMC_947902","title":"The isolation of eukaryotic ribosomal proteins. The purification and characterization of the 40 S ribosomal subunit proteins S2, S3, S4, S5, S6, S7, S8, S9, S13, S23/S24, S27, and S28.","date":"1976","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/947902","citation_count":72,"is_preprint":false},{"pmid":"2546151","id":"PMC_2546151","title":"The v-sea oncogene of avian erythroblastosis retrovirus S13: another member of the protein-tyrosine kinase gene family.","date":"1989","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/2546151","citation_count":69,"is_preprint":false},{"pmid":"25511625","id":"PMC_25511625","title":"Are cyclic lipopeptides produced by Bacillus amyloliquefaciens S13-3 responsible for the plant defence response in strawberry against Colletotrichum gloeosporioides?","date":"2015","source":"Letters in applied microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25511625","citation_count":66,"is_preprint":false},{"pmid":"2946700","id":"PMC_2946700","title":"Control of erythroid differentiation: asynchronous expression of the anion transporter and the peripheral components of the membrane skeleton in AEV- and S13-transformed cells.","date":"1986","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/2946700","citation_count":57,"is_preprint":false},{"pmid":"17881366","id":"PMC_17881366","title":"Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism.","date":"2007","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/17881366","citation_count":56,"is_preprint":false},{"pmid":"2496109","id":"PMC_2496109","title":"Gene encoding the alpha core subunit of Bacillus subtilis RNA polymerase is cotranscribed with the genes for initiation factor 1 and ribosomal proteins B, S13, S11, and L17.","date":"1989","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/2496109","citation_count":54,"is_preprint":false},{"pmid":"2437527","id":"PMC_2437527","title":"RNA-protein cross-linking in Escherichia coli 30S ribosomal subunits; determination of sites on 16S RNA that are cross-linked to proteins S3, S4, S5, S7, S8, S9, S11, S13, S19 and S21 by treatment with methyl p-azidophenyl acetimidate.","date":"1987","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/2437527","citation_count":53,"is_preprint":false},{"pmid":"2459390","id":"PMC_2459390","title":"Probing the assembly of the 3' major domain of 16 S rRNA. 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Sequence analysis of the longer unique pyrimidine oligonucleotides of bacteriophage S13 DNA by a method using unlabeled atarting oligonucleotides.","date":"1976","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/779845","citation_count":2,"is_preprint":false},{"pmid":"11479385","id":"PMC_11479385","title":"RNA editing of the ribosomal protein S13 transcripts in magnolia and sunflower mitochondria.","date":"2001","source":"Plant & cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/11479385","citation_count":1,"is_preprint":false},{"pmid":"17428396","id":"PMC_17428396","title":"[Prokaryotic expression and purification of RPS13 and preparation of polyclonal antibody against RPS13].","date":"2007","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/17428396","citation_count":1,"is_preprint":false},{"pmid":"36993679","id":"PMC_36993679","title":"MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features.","date":"2023","source":"Research square","url":"https://pubmed.ncbi.nlm.nih.gov/36993679","citation_count":1,"is_preprint":false},{"pmid":"33368645","id":"PMC_33368645","title":"Distribution of amoebal endosymbiotic environmental chlamydia Neochlamydia S13 via amoebal cytokinesis.","date":"2021","source":"Microbiology and immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33368645","citation_count":1,"is_preprint":false},{"pmid":"10390155","id":"PMC_10390155","title":"Unique features of Chinese hamster S13 gene relative to its human and Xenopus analogs.","date":"1999","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/10390155","citation_count":1,"is_preprint":false},{"pmid":"1385208","id":"PMC_1385208","title":"Immunologic characterization of jird lymphocyte responsiveness to Brugia pahangi ribosomal protein S13.","date":"1992","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/1385208","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":43517,"output_tokens":4238,"usd":0.09706,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12099,"output_tokens":4054,"usd":0.080922,"stage2_stop_reason":"end_turn"},"total_usd":0.177982,"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\": 2007,\n      \"finding\": \"Human RPS13 specifically binds to a fragment of its own pre-mRNA encompassing exons 1 and 2, intron 1, and part of intron 2, and inhibits splicing of intron 1 in vitro, providing ribonuclease protection at sequences near the 5' and 3' splice sites; this constitutes a feedback autoregulatory mechanism controlling RPS13 expression at the splicing step.\",\n      \"method\": \"In vitro splicing inhibition assay with recombinant rpS13; RNase protection mapping of protein-binding sites on pre-mRNA; transfection of HEK 293 cells with minigene containing intron 1\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal methods (in vitro binding, RNase protection, cell-based minigene assay) in single study; specificity confirmed with rpS10 and rpS16 controls\",\n      \"pmids\": [\"17881366\", \"17380891\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Overexpression of human RPS13 in gastric cancer cells (SGC7901) promotes multidrug resistance by suppressing drug-induced apoptosis and significantly increasing Bcl-2 expression and Bcl-2/Bax ratio, without altering drug accumulation or protein synthesis rates.\",\n      \"method\": \"Genetic overexpression of RPS13 in gastric cancer cells; cell viability and apoptosis assays; Western blot for Bcl-2/Bax; [3H]leucine incorporation; intracellular drug accumulation measurement\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — multiple functional assays in single lab, gain-of-function with defined molecular readout (Bcl-2/Bax ratio)\",\n      \"pmids\": [\"15149863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RPS13 promotes gastric cancer cell growth and G1-to-S phase transition by down-regulating p27(Kip1) expression and reducing CDK2 kinase activity, without altering cyclin D, cyclin E, CDK2, CDK4, or p16(INK4A) levels.\",\n      \"method\": \"RPS13 overexpression and RNAi knockdown in gastric cancer cells; cell cycle analysis by flow cytometry; Western blot for cell cycle regulators; CDK2 kinase activity assay; in vivo tumor formation assay\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal gain- and loss-of-function with multiple orthogonal readouts in single lab\",\n      \"pmids\": [\"19912438\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"E. coli ribosomal protein S13 (bacterial ortholog of RPS13/uS15) is required for ribosome subunit association, translation initiation, and translocation; targeted mutagenesis of S13 bridge contact elements and tRNA contact elements (C-terminal extension) each individually impair translational fidelity and efficiency, indicating S13 provides signal transduction between the tRNA-binding site and the small subunit head during translocation.\",\n      \"method\": \"rpsM(S13)-deficient E. coli strain; in vitro subunit association, initiation, and translocation assays; targeted mutagenesis of bridge and tRNA contact residues\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution assays combined with targeted mutagenesis, multiple functional readouts in single rigorous study\",\n      \"pmids\": [\"15876367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"In the 30S ribosomal subunit assembly map, S13 (bacterial ortholog) requires prior association of S7 (not S20 as previously mapped) for binding to the 16S rRNA ribonucleoprotein particle, placing S13 in the S7 assembly branch consistent with its head location; S13 also makes cooperative interactions with other S7-branch proteins.\",\n      \"method\": \"Base-specific chemical footprinting; primer extension analysis; single protein addition and omission studies\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple footprinting approaches in single lab correcting prior assembly map placement\",\n      \"pmids\": [\"15525707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"E. coli ribosomal protein S13 (bacterial ortholog) is cross-linked to proteins S19 in the 30S subunit, with the cross-link site identified at Cys84 of S13 and His68 of S19 by diepoxybutane cross-linking followed by peptide sequencing, FAB-MS, and amino acid analysis.\",\n      \"method\": \"Bifunctional cross-linker diepoxybutane treatment of 30S subunits; HPLC purification of cross-linked S13–S19 complex; enzymatic fragmentation; sequence analysis; FAB-MS\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-level identification of cross-link site by peptide sequencing and MS, replicated in Bacillus stearothermophilus (PMID 3291949)\",\n      \"pmids\": [\"3279034\", \"3291949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"E. coli ribosomal protein S13 has two separable functional domains: a C-terminal fragment (residues 84–117) retains 16S rRNA-binding activity at multiple sites, while the N-terminal region is important for association with protein S19, as demonstrated by proteolytic cleavage and filter-binding assays.\",\n      \"method\": \"Proteolytic cleavage of S13 into two polypeptides; nitrocellulose filter-binding assay for RNA binding; S19 competition binding assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain dissection with in vitro binding assays, single lab\",\n      \"pmids\": [\"3903659\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Directed hydroxyl radical probing from Fe(II) tethered to Cys84 of E. coli S13 (bacterial ortholog) in reconstituted 30S subunits localizes S13 adjacent to two regions of 16S rRNA: nucleotides 1308–1333 in the 3' major domain and the 950/1230 helix.\",\n      \"method\": \"In vitro reconstitution of 30S subunits with Fe(II)-EDTA derivatized S13; hydroxyl radical cleavage mapping of 16S rRNA\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — site-specific tethered cleavage in reconstituted subunit, rigorous localization of protein–RNA contacts\",\n      \"pmids\": [\"8718688\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1987,\n      \"finding\": \"E. coli ribosomal protein S13 (bacterial ortholog) is cross-linked to 16S rRNA at oligonucleotide positions 1337–1338 and anomalously at positions 189–191 in the 30S subunit, using methyl p-azidophenyl acetimidate photo-cross-linking.\",\n      \"method\": \"Photo-cross-linking with methyl p-azidophenyl acetimidate; partial nuclease digestion; isolation of RNA–protein complexes; RNA and protein analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct RNA–protein cross-linking with site identification, single study\",\n      \"pmids\": [\"2437527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"Ribosomal proteins S2, S3, S10, S13, and S14 bind to the 3' major domain of 16S rRNA; S13 and S14 each protect distinct nucleotides adjacent to regions previously protected by S19, as revealed by chemical and enzymatic probing during assembly of the 30S subunit.\",\n      \"method\": \"Chemical and enzymatic probing of 16S rRNA during stepwise assembly; monospecific and cooperative protection pattern analysis\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic probing during assembly, multiple proteins and conditions, single lab\",\n      \"pmids\": [\"2459390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1981,\n      \"finding\": \"Rat liver ribosomal protein S13 specifically binds to 5.8S rRNA with a single binding site per RNA molecule and an apparent association constant in the range of 0.2–18 × 10^5 M^-1 (measured at 4°C and 22°C), as determined by nitrocellulose membrane filtration.\",\n      \"method\": \"Nitrocellulose membrane filter binding assay with purified rat liver rpS13 and 5.8S rRNA; saturation binding and stoichiometry analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct binding assay with defined stoichiometry, single lab, single method\",\n      \"pmids\": [\"7251593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"A C-terminal truncation of E. coli S13 (rpsM mutation removing 19 C-terminal amino acids, including the RNA-binding C-terminal domain) causes decreased translational step time, reduced growth rate, and strong antisuppression of amber and opal suppressors, consistent with impaired ribosomal function; the truncated small subunit shows reduced sedimentation but forms apparently normal 70S ribosomes.\",\n      \"method\": \"Cloning and sequencing of rpsM mutation; sucrose gradient ultracentrifugation; suppressor activity assays in vivo\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical characterization of defined loss-of-function allele, multiple phenotypic readouts\",\n      \"pmids\": [\"8193163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Drosophila RpS13 is required for germline stem cell self-renewal and differentiation in the testis niche; knockdown of RpS13 affects cell proliferation and apoptosis and modulates expression of ribosome subunits, Rho1, DE-cad (E-cadherin), and Armadillo (β-catenin); Rho1 overexpression phenocopies RpS13 loss, placing RpS13 upstream of Rho1-mediated cell adhesion signaling.\",\n      \"method\": \"Tissue-specific RNAi knockdown in Drosophila testes and S2 cells; immunofluorescence for stem cell markers; TUNEL/flow cytometry for apoptosis; qRT-PCR; genetic epistasis with Rho1\",\n      \"journal\": \"Cell proliferation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — genetic epistasis with multiple readouts, single lab, Drosophila ortholog\",\n      \"pmids\": [\"32896929\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Loss-of-function P-element insertion in Drosophila RpS13 (encoding the Drosophila ortholog of ribosomal protein S13) causes the Minute phenotype (short thin bristles, slow development) and reduces RPS13 transcript to ~50%; the phenotype is rescued by P-element remobilization, establishing this as a classical Minute ribosomal protein gene.\",\n      \"method\": \"P-element mutagenesis; sequencing of interrupted gene; Northern blot quantification of transcript; genetic rescue by P-element excision\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct insertion mutagenesis with genetic rescue, single lab\",\n      \"pmids\": [\"8725235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Protein S13 (DNP-labeled) in reconstituted E. coli 30S subunits is localized by immune electron microscopy to the subunit head above the platform and on the surface facing the large subunit, confirming its position at the subunit interface.\",\n      \"method\": \"Dinitrophenylation of S13; total reconstitution of 30S subunits with DNP-S13; immune electron microscopy with anti-DNP antibodies\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct structural localization by immune EM in reconstituted particles, single lab\",\n      \"pmids\": [\"8360163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Mg2+ ions (at concentrations 0.5–20 mM) reduce the affinity of human rpS13 for the central domain fragment of 18S rRNA by inducing structural rearrangements in helices H20 and H22 of the 18S rRNA central domain that mimic the conformation found in assembled 40S subunits, as detected by hydroxyl radical probing.\",\n      \"method\": \"In vitro binding of recombinant human rpS13 to 18S rRNA central domain RNA; hydroxyl radical probing of RNA structure at varying Mg2+ concentrations\",\n      \"journal\": \"Molekuliarnaia biologiia\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single biochemical method, single lab, limited mechanistic follow-up\",\n      \"pmids\": [\"23705505\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"U14 small nucleolar RNAs (snoRNAs) are encoded within introns 3 and 5 of the human RPS13 gene, identified by PCR cloning and sequencing of the intron-containing genomic locus; the gene structure comprises 6 exons and 5 introns spanning 3.3 kb.\",\n      \"method\": \"PCR cloning and sequencing of intron-containing human S13 genomic gene; sequence comparison with Xenopus U14 snoRNA genes\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct genomic sequencing establishing structural organization, replicated feature across species\",\n      \"pmids\": [\"8920921\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPS13 (uS15) is a conserved small ribosomal subunit protein that occupies the head region of the 40S/30S subunit, contacts 16S/18S rRNA in the 3' major domain and 5.8S rRNA, bridges the inter-subunit interface through interactions with the large subunit and P-site tRNA via its C-terminal extension, and is required for subunit association, translation initiation, and translocation fidelity; in addition, free RPS13 protein feeds back to inhibit splicing of its own pre-mRNA at intron 1 as an autoregulatory mechanism, and in cancer cells elevated RPS13 suppresses apoptosis by upregulating Bcl-2/Bax and promotes cell cycle progression by down-regulating p27(Kip1).\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPS13 (uS15) is a conserved small ribosomal subunit protein of the 40S/30S head whose direct RNA contacts and inter-subunit position underpin core steps of translation [#3, #7]. It binds the 3' major domain of 16S/18S rRNA (contacting nucleotides ~1308–1338 and the 950/1230 helix) through its C-terminal RNA-binding domain, while the eukaryotic protein also binds 5.8S rRNA, establishing it as a multivalent rRNA-binding protein within the subunit head [#7, #8, #10, #6]. During 30S assembly it joins via the S7 branch and makes cooperative contacts with neighboring head proteins, including a defined cross-link to S19 mediated by its N-terminal region [#4, #9, #5, #6]. Functionally, RPS13 is required for subunit association, translation initiation, and translocation: its bridge contacts and tRNA-contacting C-terminal extension transmit signals between the tRNA-binding site and the subunit head, and truncation of the C-terminus impairs translational step time and fidelity [#3, #11, #14]. Beyond the ribosome, free RPS13 protein binds its own pre-mRNA and inhibits splicing of intron 1, constituting a feedback autoregulatory loop controlling its expression [#0]. In Drosophila the gene behaves as a classical Minute locus required for normal growth and for germline stem cell self-renewal, acting upstream of Rho1-mediated adhesion signaling [#13, #12]. In gastric cancer cells, elevated RPS13 suppresses drug-induced apoptosis by raising the Bcl-2/Bax ratio and drives G1-to-S progression by down-regulating p27(Kip1) and reducing CDK2 activity [#1, #2].\",\n  \"teleology\": [\n    {\n      \"year\": 1981,\n      \"claim\": \"Established that the eukaryotic protein has intrinsic rRNA-binding specificity by showing direct, stoichiometric binding to 5.8S rRNA, distinguishing it from purely bacterial-defined contacts.\",\n      \"evidence\": \"Nitrocellulose filter binding of purified rat liver rpS13 to 5.8S rRNA with stoichiometry analysis\",\n      \"pmids\": [\"7251593\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding site on 5.8S rRNA not mapped at nucleotide resolution\", \"Functional consequence within assembled 60S/80S not addressed\"]\n    },\n    {\n      \"year\": 1985,\n      \"claim\": \"Resolved the domain architecture of the protein, showing RNA binding and inter-protein contact map to separable regions.\",\n      \"evidence\": \"Proteolytic dissection of E. coli S13 with filter-binding and S19 competition assays\",\n      \"pmids\": [\"3903659\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Residue-level boundaries of the two functions not defined\", \"Bacterial ortholog; eukaryotic domain map inferred\"]\n    },\n    {\n      \"year\": 1987,\n      \"claim\": \"Mapped direct protein–rRNA cross-link sites, anchoring S13 to specific 16S rRNA positions.\",\n      \"evidence\": \"Photo-cross-linking with methyl p-azidophenyl acetimidate and nuclease mapping in 30S subunits\",\n      \"pmids\": [\"2437527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Anomalous 189–191 cross-link unexplained\", \"Single cross-linking chemistry\"]\n    },\n    {\n      \"year\": 1988,\n      \"claim\": \"Defined the head-region neighbor of S13 by identifying its protein partner and the precise cross-link residues, and placed it among 3' major domain binders.\",\n      \"evidence\": \"Diepoxybutane cross-linking with peptide sequencing/FAB-MS (S13–S19), plus assembly probing of the 3' major domain\",\n      \"pmids\": [\"3279034\", \"3291949\", \"2459390\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional significance of the S13–S19 contact not tested\", \"Eukaryotic equivalence of partner contact not shown\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Linked the C-terminal RNA-binding domain to translational performance by phenotyping a defined truncation allele.\",\n      \"evidence\": \"rpsM C-terminal truncation in E. coli; sucrose gradients and suppressor activity assays\",\n      \"pmids\": [\"8193163\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular step defect not isolated in vitro\", \"Effect on initiation versus elongation not separated\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Localized the protein within the 16S rRNA tertiary fold and within the subunit by tethered cleavage and immune EM, and revealed that the gene host encodes intronic U14 snoRNAs.\",\n      \"evidence\": \"Fe(II)-tethered hydroxyl radical probing from Cys84; immune EM of reconstituted 30S; genomic sequencing of the human S13 locus\",\n      \"pmids\": [\"8718688\", \"8360163\", \"8920921\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether U14 processing depends on RPS13 transcription/splicing not tested\", \"Interface position confirmed structurally but functional bridging assayed later\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Established the gene as a haploinsufficient growth determinant, the classical Minute phenotype, by mutagenesis and genetic rescue.\",\n      \"evidence\": \"P-element insertion in Drosophila RpS13 with Northern quantification and rescue by excision\",\n      \"pmids\": [\"8725235\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking reduced ribosomal protein to bristle/growth phenotype not dissected\", \"Drosophila ortholog\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Refined the 30S assembly pathway, reassigning S13 dependency from S20 to S7 and showing cooperative head-protein interactions.\",\n      \"evidence\": \"Chemical footprinting and single-protein addition/omission assembly studies\",\n      \"pmids\": [\"15525707\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinetics of assembly not measured\", \"Eukaryotic assembly order not addressed\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Connected RPS13 dosage to cancer cell survival, showing overexpression confers multidrug resistance via apoptosis suppression independent of translation rate.\",\n      \"evidence\": \"RPS13 overexpression in SGC7901 gastric cancer cells; apoptosis assays, Bcl-2/Bax Western, drug accumulation and [3H]leucine incorporation\",\n      \"pmids\": [\"15149863\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between RPS13 and Bcl-2 regulation unknown\", \"Single cell line\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Defined the core ribosomal mechanism of the protein, demonstrating it transmits signals between the tRNA site and subunit head during translocation through distinct bridge and tRNA-contact elements.\",\n      \"evidence\": \"rpsM-deficient E. coli with in vitro association/initiation/translocation assays and targeted mutagenesis\",\n      \"pmids\": [\"15876367\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Real-time conformational coupling not visualized\", \"Eukaryotic translocation role inferred from bacterial ortholog\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Revealed a non-ribosomal autoregulatory function, showing free RPS13 protein binds its own pre-mRNA and inhibits intron 1 splicing.\",\n      \"evidence\": \"In vitro splicing inhibition, RNase protection mapping, and minigene assays in HEK293 with rpS10/rpS16 specificity controls\",\n      \"pmids\": [\"17881366\", \"17380891\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular threshold of free RPS13 triggering autoregulation not quantified\", \"Spliceosomal factors involved not identified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Extended the oncogenic role to cell cycle control, showing RPS13 drives G1/S transition via p27(Kip1) down-regulation and reduced CDK2 activity.\",\n      \"evidence\": \"Reciprocal overexpression/knockdown in gastric cancer cells; flow cytometry, Western blots, CDK2 kinase assay, in vivo tumor formation\",\n      \"pmids\": [\"19912438\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of p27 regulation by RPS13 unresolved\", \"Whether effect is ribosome-dependent not addressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Probed how rRNA conformation gates RPS13 binding, showing Mg2+-induced 18S rearrangements lower its affinity.\",\n      \"evidence\": \"In vitro binding of recombinant human rpS13 to 18S central domain with hydroxyl radical probing at varying Mg2+\",\n      \"pmids\": [\"23705505\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single biochemical method without independent confirmation\", \"Physiological relevance during assembly not established\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed RPS13 in a developmental signaling context, showing it controls germline stem cell self-renewal upstream of Rho1-mediated adhesion.\",\n      \"evidence\": \"Tissue-specific RNAi in Drosophila testes/S2 cells with stem cell markers, apoptosis assays, qRT-PCR, and Rho1 epistasis\",\n      \"pmids\": [\"32896929\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the role is extraribosomal or via translation not separated\", \"Direct link to Rho1/cadherin pathway not biochemically defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved whether the cancer-associated apoptosis and cell-cycle phenotypes and the Drosophila adhesion role reflect extraribosomal moonlighting functions of RPS13 or downstream consequences of altered ribosome biogenesis/translation.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct molecular targets identified for the apoptosis/cell-cycle effects\", \"Extraribosomal versus ribosomal contributions not separated\", \"No human structural model of RPS13 within 40S in this corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [7, 8, 10, 6, 0]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [3, 14]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [3, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [3, 14, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72766\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"40S/30S small ribosomal subunit\"],\n    \"partners\": [\"RPS19\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}