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P05756

- RS13_YEAST

UniProt

P05756 - RS13_YEAST

Protein

40S ribosomal protein S13

Gene

RPS13

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 139 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    GO - Molecular functioni

    1. small ribosomal subunit rRNA binding Source: SGD
    2. structural constituent of ribosome Source: SGD

    GO - Biological processi

    1. cytoplasmic translation Source: SGD
    2. maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD

    Keywords - Molecular functioni

    Ribonucleoprotein, Ribosomal protein

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29671-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 S13
    Alternative name(s):
    S27a
    YS15
    Gene namesi
    Name:RPS13
    Synonyms:RPS13C
    Ordered Locus Names:YDR064W
    ORF Names:D4252, YD9609.18
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    SGDiS000002471. RPS13.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytosolic small ribosomal subunit Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 15115040S ribosomal protein S13PRO_0000115689Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei32 – 321Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP05756.
    PaxDbiP05756.
    PeptideAtlasiP05756.
    PRIDEiP05756.

    Expressioni

    Gene expression databases

    GenevestigatoriP05756.

    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

    BioGridi32119. 148 interactions.
    IntActiP05756. 54 interactions.
    MINTiMINT-8285180.
    STRINGi4932.YDR064W.

    Structurei

    Secondary structure

    1
    151
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 74
    Helixi30 – 4112
    Turni42 – 443
    Helixi47 – 5711
    Helixi63 – 664
    Beta strandi67 – 693
    Helixi71 – 777
    Helixi86 – 10419
    Helixi109 – 13123
    Helixi143 – 1508

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K5Xmodel-O66-130[»]
    1S1Helectron microscopy11.70O66-130[»]
    1VW9electron microscopy6.10O1-151[»]
    1VWVelectron microscopy6.10O1-151[»]
    3IZBelectron microscopy-O1-151[»]
    3O2ZX-ray4.00G1-151[»]
    3O30X-ray4.00G1-151[»]
    3U5CX-ray3.00N1-151[»]
    3U5GX-ray3.00N1-151[»]
    4BYLelectron microscopy4.30N1-151[»]
    4BYTelectron microscopy6.60N1-151[»]
    4CUYelectron microscopy3.70N2-151[»]
    ProteinModelPortaliP05756.
    SMRiP05756. Positions 2-151.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP05756.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribosomal protein S15P family.Curated

    Phylogenomic databases

    eggNOGiCOG0184.
    GeneTreeiENSGT00390000017491.
    HOGENOMiHOG000180723.
    KOiK02953.
    OMAiNWKYESA.
    OrthoDBiEOG7NW6NN.

    Family and domain databases

    HAMAPiMF_01343_A. Ribosomal_S15_A.
    InterProiIPR012606. Ribosomal_S13/S15_N.
    IPR000589. Ribosomal_S15.
    IPR023029. Ribosomal_S15P.
    IPR009068. S15_NS1_RNA-bd.
    [Graphical view]
    PfamiPF08069. Ribosomal_S13_N. 1 hit.
    PF00312. Ribosomal_S15. 1 hit.
    [Graphical view]
    SUPFAMiSSF47060. SSF47060. 1 hit.
    PROSITEiPS00362. RIBOSOMAL_S15. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P05756-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGRMHSAGKG ISSSAIPYSR NAPAWFKLSS ESVIEQIVKY ARKGLTPSQI    50
    GVLLRDAHGV TQARVITGNK IMRILKSNGL APEIPEDLYY LIKKAVSVRK 100
    HLERNRKDKD AKFRLILIES RIHRLARYYR TVAVLPPNWK YESATASALV 150
    N 151
    Length:151
    Mass (Da):17,029
    Last modified:January 23, 2007 - v3
    Checksum:i9AA9EFBEC837053D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti25 – 251W → G AA sequence (PubMed:6814480)Curated
    Sequence conflicti32 – 321S → C AA sequence (PubMed:6814480)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X84162 Genomic DNA. Translation: CAA58980.1.
    Z49209 Genomic DNA. Translation: CAA89093.1.
    Z74360 Genomic DNA. Translation: CAA98882.1.
    BK006938 Genomic DNA. Translation: DAA11910.1.
    PIRiS54048.
    RefSeqiNP_010349.3. NM_001180372.3.

    Genome annotation databases

    EnsemblFungiiYDR064W; YDR064W; YDR064W.
    GeneIDi851636.
    KEGGisce:YDR064W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X84162 Genomic DNA. Translation: CAA58980.1 .
    Z49209 Genomic DNA. Translation: CAA89093.1 .
    Z74360 Genomic DNA. Translation: CAA98882.1 .
    BK006938 Genomic DNA. Translation: DAA11910.1 .
    PIRi S54048.
    RefSeqi NP_010349.3. NM_001180372.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1K5X model - O 66-130 [» ]
    1S1H electron microscopy 11.70 O 66-130 [» ]
    1VW9 electron microscopy 6.10 O 1-151 [» ]
    1VWV electron microscopy 6.10 O 1-151 [» ]
    3IZB electron microscopy - O 1-151 [» ]
    3O2Z X-ray 4.00 G 1-151 [» ]
    3O30 X-ray 4.00 G 1-151 [» ]
    3U5C X-ray 3.00 N 1-151 [» ]
    3U5G X-ray 3.00 N 1-151 [» ]
    4BYL electron microscopy 4.30 N 1-151 [» ]
    4BYT electron microscopy 6.60 N 1-151 [» ]
    4CUY electron microscopy 3.70 N 2-151 [» ]
    ProteinModelPortali P05756.
    SMRi P05756. Positions 2-151.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32119. 148 interactions.
    IntActi P05756. 54 interactions.
    MINTi MINT-8285180.
    STRINGi 4932.YDR064W.

    Proteomic databases

    MaxQBi P05756.
    PaxDbi P05756.
    PeptideAtlasi P05756.
    PRIDEi P05756.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR064W ; YDR064W ; YDR064W .
    GeneIDi 851636.
    KEGGi sce:YDR064W.

    Organism-specific databases

    SGDi S000002471. RPS13.

    Phylogenomic databases

    eggNOGi COG0184.
    GeneTreei ENSGT00390000017491.
    HOGENOMi HOG000180723.
    KOi K02953.
    OMAi NWKYESA.
    OrthoDBi EOG7NW6NN.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29671-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 P05756.
    NextBioi 969194.
    PROi P05756.

    Gene expression databases

    Genevestigatori P05756.

    Family and domain databases

    HAMAPi MF_01343_A. Ribosomal_S15_A.
    InterProi IPR012606. Ribosomal_S13/S15_N.
    IPR000589. Ribosomal_S15.
    IPR023029. Ribosomal_S15P.
    IPR009068. S15_NS1_RNA-bd.
    [Graphical view ]
    Pfami PF08069. Ribosomal_S13_N. 1 hit.
    PF00312. Ribosomal_S15. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47060. SSF47060. 1 hit.
    PROSITEi PS00362. RIBOSOMAL_S15. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence analysis of a 32,500 bp region of the right arm of Saccharomyces cerevisiae chromosome IV."
      Brandt P., Ramlow S., Otto B., Bloecker H.
      Yeast 12:85-90(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Isolation of seventeen proteins and amino-terminal amino acid sequences of eight proteins from cytoplasmic ribosomes of yeast."
      Otaka E., Higo K., Osawa S.
      Biochemistry 21:4545-4550(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-41.
    5. "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.
    6. "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.
    7. "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 SER-32, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "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].
    9. "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 66-130, ELECTRON MICROSCOPY.
    10. "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 66-130, ELECTRON MICROSCOPY.

    Entry informationi

    Entry nameiRS13_YEAST
    AccessioniPrimary (citable) accession number: P05756
    Secondary accession number(s): D6VS50
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1988
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 139 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    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 IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3