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P05750

- RS3_YEAST

UniProt

P05750 - RS3_YEAST

Protein

40S ribosomal protein S3

Gene

RPS3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 157 (01 Oct 2014)
      Sequence version 5 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    GO - Molecular functioni

    1. DNA-(apurinic or apyrimidinic site) lyase activity Source: SGD
    2. RNA binding Source: UniProtKB-KW
    3. structural constituent of ribosome Source: SGD

    GO - Biological processi

    1. cytoplasmic translation Source: SGD
    2. DNA catabolic process, endonucleolytic Source: GOC
    3. ribosomal small subunit export from nucleus Source: SGD
    4. rRNA export from nucleus Source: SGD

    Keywords - Molecular functioni

    Ribonucleoprotein, Ribosomal protein

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33190-MONOMER.
    ReactomeiREACT_188965. SRP-dependent cotranslational protein targeting to membrane.
    REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_217188. Formation of a pool of free 40S subunits.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    40S ribosomal protein S3
    Alternative name(s):
    RP13
    YS3
    Gene namesi
    Name:RPS3
    Synonyms:SUF14
    Ordered Locus Names:YNL178W
    ORF Names:N1653
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIV

    Organism-specific databases

    SGDiS000005122. RPS3.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytosolic small ribosomal subunit Source: SGD
    2. preribosome, small subunit precursor Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed3 Publications
    Chaini2 – 24023940S ribosomal protein S3PRO_0000130332Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei44 – 441Phosphothreonine1 Publication
    Modified residuei70 – 701Phosphothreonine1 Publication
    Modified residuei97 – 971Phosphoserine1 Publication
    Modified residuei129 – 1291Phosphoserine1 Publication
    Cross-linki212 – 212Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Modified residuei221 – 2211Phosphoserine4 Publications
    Modified residuei231 – 2311Phosphothreonine1 Publication

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP05750.
    PaxDbiP05750.
    PeptideAtlasiP05750.
    PRIDEiP05750.

    2D gel databases

    UCD-2DPAGEP05750.

    Expressioni

    Gene expression databases

    GenevestigatoriP05750.

    Interactioni

    Subunit structurei

    Component of the small ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains 32 different proteins (encoded by 56 genes) and 1 molecule of RNA (18S). The 60S subunit contains 46 different proteins (encoded by 81 genes) and 3 molecules of RNA (25S, 5.8S and 5S).1 Publication

    Protein-protein interaction databases

    BioGridi35653. 148 interactions.
    DIPiDIP-4328N.
    IntActiP05750. 98 interactions.
    MINTiMINT-512497.
    STRINGi4932.YNL178W.

    Structurei

    Secondary structure

    1
    240
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi15 – 2814
    Turni29 – 335
    Beta strandi34 – 429
    Beta strandi45 – 539
    Helixi55 – 595
    Turni60 – 634
    Helixi64 – 7714
    Beta strandi83 – 908
    Helixi94 – 963
    Helixi98 – 11013
    Helixi115 – 12814
    Beta strandi134 – 1418
    Beta strandi142 – 1465
    Beta strandi152 – 1598
    Helixi163 – 1675
    Beta strandi168 – 1769
    Beta strandi181 – 1899
    Helixi192 – 1943
    Beta strandi196 – 1983
    Beta strandi222 – 2243

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K5Xmodel-C6-193[»]
    1S1Helectron microscopy11.70C2-193[»]
    1VW9electron microscopy6.10E1-240[»]
    1VWVelectron microscopy6.10E1-240[»]
    3IZBelectron microscopy-B1-240[»]
    3O2ZX-ray4.00C1-240[»]
    3O30X-ray4.00C1-240[»]
    3U5CX-ray3.00D1-240[»]
    3U5GX-ray3.00D1-240[»]
    4BSZX-ray2.84A1-240[»]
    4BYLelectron microscopy4.30D1-240[»]
    4BYTelectron microscopy6.60D1-240[»]
    4CUYelectron microscopy3.70D4-225[»]
    ProteinModelPortaliP05750.
    SMRiP05750. Positions 3-225.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP05750.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini21 – 9272KH type-2PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the ribosomal protein S3P family.Curated
    Contains 1 KH type-2 domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0092.
    GeneTreeiENSGT00390000008610.
    HOGENOMiHOG000210611.
    KOiK02985.
    OMAiYADGFMI.
    OrthoDBiEOG780RZC.

    Family and domain databases

    Gene3Di3.30.1140.32. 1 hit.
    InterProiIPR004087. KH_dom.
    IPR004044. KH_dom_type_2.
    IPR009019. KH_prok-type.
    IPR001351. Ribosomal_S3_C.
    IPR018280. Ribosomal_S3_CS.
    IPR005703. Ribosomal_S3_euk/arc.
    [Graphical view]
    PfamiPF07650. KH_2. 1 hit.
    PF00189. Ribosomal_S3_C. 1 hit.
    [Graphical view]
    SMARTiSM00322. KH. 1 hit.
    [Graphical view]
    SUPFAMiSSF54814. SSF54814. 1 hit.
    SSF54821. SSF54821. 1 hit.
    TIGRFAMsiTIGR01008. rpsC_E_A. 1 hit.
    PROSITEiPS50823. KH_TYPE_2. 1 hit.
    PS00548. RIBOSOMAL_S3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P05750-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVALISKKRK LVADGVFYAE LNEFFTRELA EEGYSGVEVR VTPTKTEVII    50
    RATRTQDVLG ENGRRINELT LLVQKRFKYA PGTIVLYAER VQDRGLSAVA 100
    QAESMKFKLL NGLAIRRAAY GVVRYVMESG AKGCEVVVSG KLRAARAKAM 150
    KFADGFLIHS GQPVNDFIDT ATRHVLMRQG VLGIKVKIMR DPAKSRTGPK 200
    ALPDAVTIIE PKEEEPILAP SVKDYRPAEE TEAQAEPVEA 240
    Length:240
    Mass (Da):26,503
    Last modified:January 23, 2007 - v5
    Checksum:iB85C0DFEB011745F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti17 – 171F → N in AAA35010. 1 PublicationCurated
    Sequence conflicti223 – 2242KD → NH in AAA35010. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U34347 Genomic DNA. Translation: AAC49380.1.
    D25285 mRNA. Translation: BAA04973.1.
    L31405 Genomic DNA. Translation: AAA35010.1.
    Z71454 Genomic DNA. Translation: CAA96070.1.
    BK006947 Genomic DNA. Translation: DAA10373.1.
    PIRiS48510.
    RefSeqiNP_014221.3. NM_001183016.3.

    Genome annotation databases

    EnsemblFungiiYNL178W; YNL178W; YNL178W.
    GeneIDi855543.
    KEGGisce:YNL178W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U34347 Genomic DNA. Translation: AAC49380.1 .
    D25285 mRNA. Translation: BAA04973.1 .
    L31405 Genomic DNA. Translation: AAA35010.1 .
    Z71454 Genomic DNA. Translation: CAA96070.1 .
    BK006947 Genomic DNA. Translation: DAA10373.1 .
    PIRi S48510.
    RefSeqi NP_014221.3. NM_001183016.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1K5X model - C 6-193 [» ]
    1S1H electron microscopy 11.70 C 2-193 [» ]
    1VW9 electron microscopy 6.10 E 1-240 [» ]
    1VWV electron microscopy 6.10 E 1-240 [» ]
    3IZB electron microscopy - B 1-240 [» ]
    3O2Z X-ray 4.00 C 1-240 [» ]
    3O30 X-ray 4.00 C 1-240 [» ]
    3U5C X-ray 3.00 D 1-240 [» ]
    3U5G X-ray 3.00 D 1-240 [» ]
    4BSZ X-ray 2.84 A 1-240 [» ]
    4BYL electron microscopy 4.30 D 1-240 [» ]
    4BYT electron microscopy 6.60 D 1-240 [» ]
    4CUY electron microscopy 3.70 D 4-225 [» ]
    ProteinModelPortali P05750.
    SMRi P05750. Positions 3-225.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35653. 148 interactions.
    DIPi DIP-4328N.
    IntActi P05750. 98 interactions.
    MINTi MINT-512497.
    STRINGi 4932.YNL178W.

    2D gel databases

    UCD-2DPAGE P05750.

    Proteomic databases

    MaxQBi P05750.
    PaxDbi P05750.
    PeptideAtlasi P05750.
    PRIDEi P05750.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YNL178W ; YNL178W ; YNL178W .
    GeneIDi 855543.
    KEGGi sce:YNL178W.

    Organism-specific databases

    SGDi S000005122. RPS3.

    Phylogenomic databases

    eggNOGi COG0092.
    GeneTreei ENSGT00390000008610.
    HOGENOMi HOG000210611.
    KOi K02985.
    OMAi YADGFMI.
    OrthoDBi EOG780RZC.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33190-MONOMER.
    Reactomei REACT_188965. SRP-dependent cotranslational protein targeting to membrane.
    REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_217188. Formation of a pool of free 40S subunits.

    Miscellaneous databases

    EvolutionaryTracei P05750.
    NextBioi 979610.
    PROi P05750.

    Gene expression databases

    Genevestigatori P05750.

    Family and domain databases

    Gene3Di 3.30.1140.32. 1 hit.
    InterProi IPR004087. KH_dom.
    IPR004044. KH_dom_type_2.
    IPR009019. KH_prok-type.
    IPR001351. Ribosomal_S3_C.
    IPR018280. Ribosomal_S3_CS.
    IPR005703. Ribosomal_S3_euk/arc.
    [Graphical view ]
    Pfami PF07650. KH_2. 1 hit.
    PF00189. Ribosomal_S3_C. 1 hit.
    [Graphical view ]
    SMARTi SM00322. KH. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54814. SSF54814. 1 hit.
    SSF54821. SSF54821. 1 hit.
    TIGRFAMsi TIGR01008. rpsC_E_A. 1 hit.
    PROSITEi PS50823. KH_TYPE_2. 1 hit.
    PS00548. RIBOSOMAL_S3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The ribosomal protein gene RPS3 is an essential single copy gene of the yeast Saccharomyces cerevisiae."
      Finken-Eigen M., Domdey H., Koehrer K.
      Biochem. Biophys. Res. Commun. 223:397-403(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: DBY874.
    2. "Yeast mRNA for ribosomal protein YS3."
      Okazaki M., Suzuki K., Otaka E.
      Submitted (NOV-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
      Strain: ATCC 204508 / S288c.
    3. "Molecular cloning and analysis of the RPS3 gene of Saccharomyces cerevisiae."
      Burbee D.G., Armstrong B.C.
      Submitted (APR-1994) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
      Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
      , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
      Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    6. "Yeast ribosomal proteins. VIII. Isolation of two proteins and sequence characterization of twenty-four proteins from cytoplasmic ribosomes."
      Otaka E., Higo K., Itoh T.
      Mol. Gen. Genet. 195:544-546(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: PARTIAL PROTEIN SEQUENCE OF 2-21, CLEAVAGE OF INITIATOR METHIONINE.
    7. "NH2-terminal acetylation of ribosomal proteins of Saccharomyces cerevisiae."
      Takakura H., Tsunasawa S., Miyagi M., Warner J.R.
      J. Biol. Chem. 267:5442-5445(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-21.
    8. "The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae."
      Planta R.J., Mager W.H.
      Yeast 14:471-477(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NOMENCLATURE, SUBUNIT.
    9. "The action of N-terminal acetyltransferases on yeast ribosomal proteins."
      Arnold R.J., Polevoda B., Reilly J.P., Sherman F.
      J. Biol. Chem. 274:37035-37040(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: CLEAVAGE OF INITIATOR METHIONINE.
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-212.
      Strain: SUB592.
    12. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-221, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    13. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-70; SER-129 AND SER-221, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-44; SER-97 AND SER-221, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-221 AND THR-231, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    17. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    18. "Structure of the 80S ribosome from Saccharomyces cerevisiae -- tRNA-ribosome and subunit-subunit interactions."
      Spahn C.M.T., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J.
      Cell 107:373-386(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: 3D-STRUCTURE MODELING OF 6-193, ELECTRON MICROSCOPY.
    19. "Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation."
      Spahn C.M.T., Gomez-Lorenzo M.G., Grassucci R.A., Joergensen R., Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P.G., Frank J.
      EMBO J. 23:1008-1019(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: 3D-STRUCTURE MODELING OF 2-193, ELECTRON MICROSCOPY.

    Entry informationi

    Entry nameiRS3_YEAST
    AccessioniPrimary (citable) accession number: P05750
    Secondary accession number(s): D6W107
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1988
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 157 of the entry and version 5 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 146000 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Ribosomal proteins
      Ribosomal proteins families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome XIV
      Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

    External Data

    Dasty 3