Affinage

RPS11

Small ribosomal subunit protein uS17 · UniProt P62280

Length
158 aa
Mass
18.4 kDa
Annotated
2026-06-10
60 papers in source corpus 14 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RPS11 is a conserved small ribosomal subunit protein that localizes to the platform/central domain of the small subunit, where it directly contacts rRNA, mRNA, and tRNA to support translation (PMID:12937172, PMID:2459389, PMID:2437528, PMID:2437527). Cross-linking and chemical-probing studies place RPS11 in contact with the 693-705 and 690-720/790 loop regions of small-subunit rRNA near P-site nucleotides, assembling cooperatively with neighboring proteins S6 and S18 (PMID:2459389, PMID:2437528, PMID:2437527), and reconstitution assays establish it as directly required for tRNA binding to the small subunit (PMID:25421), with photoaffinity mapping confirming contact between the D loop of P-site tRNA and RPS11 (PMID:9292501). RPS11 also participates directly in mRNA binding, being cross-linked to mRNA within the 48S pre-initiation complex (PMID:6514574), and its physical interaction with protein S7 forms the mRNA exit channel; disrupting this interaction increases frameshifting, nonsense readthrough, and codon misreading, defining a role in translational fidelity and ribosome dynamics (PMID:12937172). RPS11 carries unusual post-translational modifications including an N-terminal isopeptide bond and near-stoichiometric isoaspartate (PMID:337304, PMID:10217780). Beyond the ribosome, human RPS11 is required for the proapoptotic response to topoisomerase II poisons, with its loss conferring resistance to etoposide and doxorubicin and impairing induction of APAF1 (PMID:32528131).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 1977 Medium

    Initial characterization revealed that RPS11 carries an unusual covalent modification, raising the question of what post-translational chemistry distinguishes this ribosomal protein.

    Evidence N-terminal protein sequencing and chemical characterization of an isopeptide bond in E. coli S11

    PMID:337304

    Open questions at the time
    • Functional consequence of the N-terminal isopeptide bond is unresolved
    • Conservation of the modification in eukaryotic RPS11 not established
  2. 1978 Medium

    Reconstitution experiments addressed whether RPS11 is functionally required for ribosome activity, showing it is directly needed for tRNA binding to the small subunit.

    Evidence Reconstitution of tetranitromethane-inactivated 30S subunits with purified S11 and phe-tRNA binding assay

    PMID:25421

    Open questions at the time
    • Single method/single lab
    • Does not localize the binding contact at nucleotide resolution
  3. 1984 Medium

    Cross-linking in the initiation complex established that RPS11 contacts mRNA, placing it within the mRNA-binding domain of the small subunit during translation initiation.

    Evidence Diepoxybutane cross-linking of native 48S pre-initiation complexes formed with labeled globin mRNA

    PMID:6514574

    Open questions at the time
    • Does not define mRNA channel residues
    • Single cross-linking method
  4. 1987 Medium

    RNA-protein cross-linking localized RPS11 to a specific rRNA region, anchoring it to the central platform domain of the small subunit.

    Evidence Chemical cross-linking to 16S rRNA positions 693-697, replicated across two independent cross-linkers

    PMID:2437527 PMID:2437528

    Open questions at the time
    • Static contact map only
    • Does not address dynamics during translation
  5. 1988 Medium

    Assembly-dependent rRNA probing showed RPS11 binds rRNA cooperatively with S6 and S18 near P-site nucleotides, integrating it into the platform assembly pathway.

    Evidence Chemical probing of 16S rRNA reactivities during 30S subunit assembly

    PMID:2459389

    Open questions at the time
    • Cooperativity inferred from probing, not structural data
    • Order of assembly events not fully resolved
  6. 1997 Medium

    Photoaffinity cross-linking resolved a direct spatial contact between P-site tRNA and RPS11, linking its platform position to tRNA accommodation.

    Evidence 4-thiouridine photoaffinity cross-linking of P-site tRNA(Phe) D loop to S11 in 70S ribosomes

    PMID:9292501

    Open questions at the time
    • Snapshot of one functional state
    • Does not quantify contribution to tRNA selection
  7. 1999 Medium

    Quantification of isoaspartate identified a second abundant modification of RPS11, extending the question of how modification chemistry affects this protein.

    Evidence Isoaspartate quantification and PIMT expression in E. coli protein fractions

    PMID:10217780

    Open questions at the time
    • Functional significance of isoaspartate unknown
    • Whether modification is regulated or stochastic damage unclear
  8. 2003 High

    Mutagenesis of the RPS11-S7 interface tied a specific physical contact to translational accuracy, defining RPS11's role in suppressing frameshifting, readthrough, and misreading via the mRNA exit channel.

    Evidence Site-directed mutagenesis with in vivo fidelity assays, toeprinting, and filter-binding

    PMID:12937172

    Open questions at the time
    • Structural basis of how the contact constrains the mRNA path not resolved
    • Eukaryotic conservation of the fidelity role not directly tested
  9. 2017 Medium

    A plant study extended RPS11 beyond core translation, showing it physically binds a viral suppressor protein and supports viral replication, implying extra-ribosomal interactions.

    Evidence Y2H, BiFC, GST pull-down and TRV gene silencing of NbRPS11 with CMV 2b in Nicotiana benthamiana

    PMID:28806733

    Open questions at the time
    • Mechanism of how RPS11 supports 2b silencing-suppressor activity unclear
    • Relevance to human RPS11 not established
  10. 2020 Medium

    A CRISPR screen revealed an unexpected requirement for human RPS11 in DNA-damage-induced apoptosis, linking it to APAF1 induction after topoisomerase II poisoning.

    Evidence Genome-scale CRISPR knockout screen with etoposide plus validation knockout and APAF1 readout in glioma cells

    PMID:32528131

    Open questions at the time
    • Whether the effect is via canonical translation or an extra-ribosomal function unresolved
    • Molecular mechanism connecting RPS11 to APAF1 transcription unknown
  11. 2025 Low

    A bacterial RPS11 was reported to induce trained immunity via TLR4-TET2 signaling, raising the possibility of immunomodulatory activity distinct from translation.

    Evidence Bioactivity-guided fractionation, Galleria model, pathway analysis, and vaccine adjuvant testing

    PMID:40381785

    Open questions at the time
    • No reconstitution or mutagenesis confirming the TLR4-TET2 pathway
    • Single lab, abstract-level mechanism only
  12. 2026 Low

    RPS11 was implicated in mitochondrial protein translation and ferroptosis suppression downstream of MSC exosomes, but the mechanism is inferred rather than directly demonstrated.

    Evidence Mitochondrial proteomics and RPS11 knockdown with ferroptosis/mitochondrial readouts in HPMECs

    PMID:42174606

    Open questions at the time
    • Link to mitochondrial translation inferred from proteomics without reconstitution
    • Direct role of cytoplasmic RPS11 in mitochondrial translation not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved whether the human extra-ribosomal roles of RPS11 (APAF1-dependent apoptosis, mitochondrial translation, ferroptosis) reflect a moonlighting function or secondary consequences of altered ribosome biogenesis, and the functional purpose of its conserved post-translational modifications is unknown.
  • No mechanism connecting ribosomal RPS11 to APAF1 transcription
  • Functional role of N-terminal isopeptide and isoaspartate modifications undefined
  • No human structural model of the RPS11-S7 exit channel in the timeline

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0005198 structural molecule activity 2
Localization
GO:0005840 ribosome 4
Partners
RPS18RPS6RPS7
Complex memberships
40S small ribosomal subunit

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2003 RPS11 (bacterial S11) physically interacts with ribosomal protein S7 at the E site of the 30S subunit, connecting the head to the platform and forming the mRNA exit channel; disruption of this interaction by site-directed mutagenesis increases frameshifting, readthrough of nonsense codons, codon misreading, and enhanced mRNA binding to 30S subunits, demonstrating a functional role in translational fidelity and ribosome dynamics. Site-directed mutagenesis, in vivo translational fidelity assays (frameshifting, readthrough, misreading), toeprinting assays, filter-binding assays The Journal of biological chemistry High 12937172
1988 RPS11 (eukaryotic S11) interacts with the 690-720 and 790 loop regions of 16S rRNA in a cooperative manner with proteins S6 and S18, as shown by chemical probing of rRNA reactivities upon protein assembly into the 30S subunit; these proteins interact with residues near P-site nucleotides in 16S rRNA. Chemical probing of 16S rRNA with chemical probes during ribosome assembly Journal of molecular biology Medium 2459389
1987 E. coli ribosomal protein S11 is cross-linked to 16S rRNA within an oligonucleotide encompassing positions 693-697, placing it in the central domain of the 30S subunit platform. RNA-protein cross-linking with bis-(2-chloroethyl)-methylamine followed by partial nuclease digestion and RNA/protein analysis Nucleic acids research Medium 2437527 2437528
1978 E. coli ribosomal proteins S1, S11, and S21 are directly required for tRNA binding to the 30S ribosome; reconstitution experiments showed that unmodified S11 restores phe-tRNA binding activity to tetranitromethane-inactivated 30S ribosomes. Ribosome reconstitution with tetranitromethane-inactivated 30S subunits and individual purified proteins, phe-tRNA binding assay Nucleic acids research Medium 25421
1984 Eukaryotic ribosomal protein S11 is cross-linked to mRNA within the 48S pre-initiation complex, identifying it as part of the mRNA-binding domain of the small ribosomal subunit during translation initiation. Chemical cross-linking with diepoxybutane of native 48S pre-initiation complexes formed with 125I-labeled globin mRNA, followed by isolation and identification of covalent mRNA-protein complexes Nucleic acids research Medium 6514574
1977 E. coli ribosomal protein S11 has a unique N-terminal isopeptide bond between N-alpha-monomethylalanine and the epsilon-amino group of the N-terminal lysine residue, creating a branching point — a post-translational modification not previously observed in ribosomal proteins. Direct protein N-terminal sequence analysis and chemical characterization of the isopeptide bond Proceedings of the National Academy of Sciences of the United States of America Medium 337304
1999 E. coli ribosomal protein S11 accumulates near-stoichiometric levels of isoaspartate (estimated 0.5 mol per mol S11) during logarithmic growth, representing a post-translational modification that may be functionally important; expression of rat PIMT in E. coli reduced isoaspartate levels in cellular proteins. Isoaspartate quantification in E. coli protein fractions, identification of isoaspartate-containing protein by mass analysis, plasmid-based expression of rat PIMT Journal of bacteriology Medium 10217780
1997 In E. coli 70S ribosomes, the D loop (nucleotide U20) of P-site bound tRNA(Phe) is directly cross-linked to ribosomal protein S11, mapping the D loop to the platform of the 30S subunit. Photoaffinity cross-linking with 4-thiouridine-substituted tRNA(Phe) at the ribosomal P site, irradiation at 300 nm, identification of cross-linked proteins RNA (New York, N.Y.) Medium 9292501
2020 Loss of human RPS11 via CRISPR knockout confers resistance to topoisomerase II poisons (etoposide and doxorubicin) in glioma cells and impairs induction of the proapoptotic gene APAF1 following treatment, establishing RPS11 as a factor required for the DNA damage-induced apoptotic response to TOP2 poisons. Genome-scale CRISPR knockout screen with etoposide, validation by individual RPS11 knockout, measurement of APAF1 expression by immunoblot/qPCR, cell viability assays Oncogene Medium 32528131
2017 Plant 30S ribosomal protein S11 (NbRPS11) physically interacts with the CMV 2b protein (LS2b); knockdown of NbRPS11 by TRV-based gene silencing reduced CMV viral RNA replication, decreased CMV infection levels, and reduced the RNA silencing suppressor activity of CMV 2b protein in Nicotiana benthamiana. Yeast two-hybrid, bimolecular fluorescence complementation (BiFC) by confocal microscopy, GST pull-down assay, TRV-based gene silencing knockdown, immunoblot analysis of viral RNA and protein levels PloS one Medium 28806733
2025 Enterococcus faecalis ribosomal protein RPS11 induces trained immunity in innate immune cells through TLR4-TET2 signaling-mediated ribosomal biogenesis inhibition, resulting in enhanced MHC molecule expression on antigen-presenting cells; RPS11 conjugated to superparamagnetic iron oxide nanoparticles boosted influenza vaccine efficacy. Bioactivity-guided fractionation, Galleria mellonella larval phenotypic model, mechanistic pathway analysis (TLR4-TET2 signaling), MHC expression measurement, in vivo vaccine efficacy testing International journal of biological macromolecules Low 40381785
2026 RPS11 knockdown in human pulmonary microvascular endothelial cells (HPMECs) blocked the ability of hUCMSC-derived exosomes to suppress ferroptosis and restore mitochondrial function; mechanistically, hUCMSC-Exos upregulate RPS11 to promote mitochondria-encoded protein translation. Proteomic sequencing of mitochondria from treated HPMECs, RPS11 knockdown, assessment of ferroptosis markers and mitochondrial function, multi-omics analysis Journal of nanobiotechnology Low 42174606
1999 Human RPS11 and RPL13A genes are tandemly located in the genome separated by only 4.6 kb, with four snoRNA genes (U32, U33, U34 in RPL13A introns; U35 in both RPL13A intron 6 and RPS11 intron 3) encoded within their introns, a conserved organization also found in mouse. Genomic sequencing and gene structure analysis of human and mouse RPS11/RPL13A loci Gene Low 10580157

Source papers

Stage 0 corpus · 60 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1986 Spinach plastid genes coding for initiation factor IF-1, ribosomal protein S11 and RNA polymerase alpha-subunit. Nucleic acids research 96 3003688
1988 Interaction of ribosomal proteins S5, S6, S11, S12, S18 and S21 with 16 S rRNA. Journal of molecular biology 94 2459389
1977 Isolation of eukaryotic ribosomal proteins. Purification and characterization of the 40 S ribosomal subunit proteins Sa, Sc, S3a, S3b, S5', S9, S10, S11, S12, S14, S15, S15', S16, S17, S18, S19, S20, S21, S26, S27', and S29. The Journal of biological chemistry 60 925037
1984 Cross-linking of mRNA to initiation factor eIF-3, 24 kDa cap binding protein and ribosomal proteins S1, S3/3a, S6 and S11 within the 48S pre-initiation complex. Nucleic acids research 58 6514574
1989 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. Journal of bacteriology 54 2496109
1987 RNA-protein cross-linking in Escherichia coli 30S ribosomal subunits; determination of sites on 16S RNA that are cross-linked to proteins S3, S4, S7, S9, S10, S11, S17, S18 and S21 by treatment with bis-(2-chloroethyl)-methylamine. Nucleic acids research 54 2437528
1987 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. Nucleic acids research 53 2437527
1990 Noncoordinated expression of S6, S11, and S14 ribosomal protein genes in leukemic blast cells. Cancer research 51 1697501
1994 The S11 and S13 self incompatibility alleles in Solanum chacoense Bitt. are remarkably similar. Plant molecular biology 45 8155878
2003 A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome. The Journal of biological chemistry 38 12937172
1996 Molecular cloning of a RNA binding protein, S1-1. Nucleic acids research 38 8760884
1985 Nucleotide sequence of cloned cDNA specific for rat ribosomal protein S11. The Journal of biological chemistry 37 3838984
2015 Identification and molecular mapping of Rps11, a novel gene conferring resistance to Phytophthora sojae in soybean. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 31 26660465
2000 Preparation and characterization of antibodies against human ribosomal proteins: heterogeneous expression of S11 and S30 in a panel of human cancer cell lines. Japanese journal of cancer research : Gann 30 10965021
2014 Cell motility and biofilm formation in Bacillus subtilis are affected by the ribosomal proteins, S11 and S21. Bioscience, biotechnology, and biochemistry 27 25035996
1999 Isoaspartate in ribosomal protein S11 of Escherichia coli. Journal of bacteriology 27 10217780
1998 Rice dwarf phytoreovirus segment S11 encodes a nucleic acid binding protein. Virology 27 9454700
1991 Nucleotide sequence and characterization of a maize cytoplasmic ribosomal protein S11 cDNA. Plant molecular biology 27 1840689
2015 Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11. Research in microbiology 25 25753102
2013 Deletion of the human cytomegalovirus US17 gene increases the ratio of genomes per infectious unit and alters regulation of immune and endoplasmic reticulum stress response genes at early and late times after infection. Journal of virology 25 24335296
2017 Construction of All-Solid-State Batteries based on a Sulfur-Graphene Composite and Li9.54 Si1.74 P1.44 S11.7 Cl0.3 Solid Electrolyte. Chemistry (Weinheim an der Bergstrasse, Germany) 23 28722816
2001 Electrophoretic characterization of ribosomal subunits and proteins in apoptosis: specific downregulation of S11 in staurosporine-treated human breast carcinoma cells. Biochemistry 23 11735401
2018 Plasmid pcDNA3.1-s11 constructed based on the S11 segment of grass carp reovirus as DNA vaccine provides immune protection. Vaccine 22 29764681
2013 Cloning, expression, and characterization of β-mannanase from Bacillus subtilis MAFIC-S11 in Pichia pastoris. Applied biochemistry and biotechnology 22 23446982
2020 Ribosomal protein S11 influences glioma response to TOP2 poisons. Oncogene 21 32528131
2016 Complete Genome Sequence of Edwardsiella piscicida Isolate S11-285 Recovered from Channel Catfish (Ictalurus punctatus) in Mississippi, USA. Genome announcements 18 27881536
2008 S1-1 nuclear domains: characterization and dynamics as a function of transcriptional activity. Biology of the cell 18 18315527
1978 Evidence that proteins S1, S11 and S21 directly participates in the binding of transfer RNA to the 30S ribosome. Nucleic acids research 17 25421
2006 Infection-dependent nuclear localization of US17, a member of the US12 family of human cytomegalovirus-encoded seven-transmembrane proteins. Journal of virology 15 16414996
1977 Isopeptide linkage between N-alpha-monomethylalanine and lysine in ribosomal protein S11 from Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 15 337304
1999 Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome. Gene 14 10580157
1988 Molecular cloning and nucleotide sequence of the gene for the ribosomal protein S11 from the archaebacterium Halobacterium marismortui. The Journal of biological chemistry 14 3182783
2016 Isolation of endosulfan sulfate-degrading Rhodococcus koreensis strain S1-1 from endosulfan contaminated soil and identification of a novel metabolite, endosulfan diol monosulfate. Biochemical and biophysical research communications 13 27073164
2005 Molecular analysis of the conserved C4 region of the S11-RNase of Solanum chacoense. Planta 13 15650838
1977 Further evidence that the ribosomal 30S proteins S3, S5, S9, S11, S12, and S18 possess specific 16S RNA binding sites. Molecular & general genetics : MGG 13 331074
2017 The interaction between endogenous 30S ribosomal subunit protein S11 and Cucumber mosaic virus LS2b protein affects viral replication, infection and gene silencing suppressor activity. PloS one 12 28806733
1991 Molecular analysis of rice dwarf phytoreovirus segment S11 corresponding to wound tumour phytoreovirus segment S12. The Journal of general virology 11 1840611
1983 Direct micro-sequence analysis of peptides from Escherichia coli ribosomal proteins S11, L9 and L29 after separation by reversed phase chromatography. Hoppe-Seyler's Zeitschrift fur physiologische Chemie 10 6341200
1983 The gene coding the human S11 surface antigens maps between the loci for HPRT and G6PD on the X-chromosome. Experimental cell research 10 6685651
2022 Optimization and Evaluation of the 30S-S11 rRNA Gene for Taxonomic Profiling of Oral Streptococci. Applied and environmental microbiology 9 35730938
2015 The analysis of meat traits of Sussex cockerels and capons (S11) at different ages. Poultry science 9 26614680
1988 Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family. FEBS letters 8 3191988
1986 On the sequence homology of the ribosomal proteins, Escherichia coli S11, yeast rp59 and Chinese hamster S14. FEBS letters 8 3522274
2013 Influence of periplasmic oxidation of glucose on pyoverdine synthesis in Pseudomonas putida S11. Applied microbiology and biotechnology 7 23392768
1993 Polymerase chain reaction and direct sequencing of Neisseria gonorrhoeae protein IB gene: partial nucleotide and amino acid sequence analysis of strains S4, S11, S48 (serovar IB4) and S34 (serovar IB5). Medical microbiology and immunology 6 8232067
2006 Improvement of carbonyl reductase production of Geotrichum candidum for the transformation of 1-acetonaphthone to S(-)-1-(1'-napthyl) ethanol. Bioresource technology 5 17027259
2022 Phosphorylation of S11 in PHR1 negatively controls its transcriptional activity. Physiologia plantarum 4 36444477
1997 Photoaffinity labeling of 30S-subunit proteins S7 and S11 by 4-thiouridine-substituted tRNA(Phe) situated at the P site of Escherichia coli ribosomes. RNA (New York, N.Y.) 4 9292501
1989 Crosslinking of ribosomal proteins S4, S5, S7, S8, S11, S12 and S18 to domains 1 and 2 of 16S rRNA in the Escherichia coli 30S particle. Biochimie 4 2505863
2025 Trained immunity driven by Enterococcus faecalis ribosomal protein S11 enhances antigen presentation and boosts influenza vaccine efficacy via nanoparticle delivery. International journal of biological macromolecules 3 40381785
2012 Influence of siderophore pyoverdine synthesis and iron-uptake on abiotic and biotic surface colonization of Pseudomonas putida S11. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 3 22821204
2012 Genome sequence of the plant growth-promoting rhizobacterium Pseudomonas putida S11. Journal of bacteriology 3 23045515
2025 Allelism of Rps3b and Rps11 revealed by NLR gene capture of resistance genes to Phytophthora sojae in soybean. The plant genome 2 40506403
2016 A cluster of 3' coterminal transcripts from US12-US17 locus of human cytomegalovirus. Virus genes 2 26931512
2002 [Effects of p-nitrophenol and organophosphorous nitroaromatic insecticides on the respiratory activity of free and immobilized cells of strains S-11 and BA-11 of Pseudomonas putida]. Prikladnaia biokhimiia i mikrobiologiia 2 12068580
2022 Genomic and metabolomic profiling of endolithic Rhodococcus fascians strain S11 isolated from an arid serpentine environment. Archives of microbiology 1 35587838
2018 ACANTHAMOEBA SP.S-11 PHAGOCYTOTIC ACTIVITY ON MYCOBACTERIUM LEPRAE IN DIFFERENT NUTRIENT CONDITIONS. African journal of infectious diseases 1 29619429
2026 E. coli-generated dsRNA targeting ribosomal protein L10, S11, and arginine kinase via oral administration impairs larval development in Tuta absoluta. Bulletin of entomological research 0 42093637
2026 hUCMSC-exosomes attenuate acute lung injury by inhibiting ferroptosis in pulmonary microvascular endothelial cells through ribosomal protein RPS11 upregulation. Journal of nanobiotechnology 0 42174606
1994 Xenopus laevis ribosomal protein S11: cloning and sequencing of the cDNA and primary structure of the protein. Biochemical and biophysical research communications 0 8093055

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