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P05756

- RS13_YEAST

UniProt

P05756 - RS13_YEAST

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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

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
Complete GO annotation...

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.
REACT_232946. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_248935. Ribosomal scanning and start codon recognition.
REACT_252688. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_257608. Formation of the ternary complex, and subsequently, the 43S complex.
REACT_257951. Peptide chain elongation.

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
Complete GO annotation...

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. 149 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 – 74Combined sources
Helixi30 – 4112Combined sources
Turni42 – 443Combined sources
Helixi47 – 5711Combined sources
Helixi63 – 664Combined sources
Beta strandi67 – 693Combined sources
Helixi71 – 777Combined sources
Helixi86 – 10419Combined sources
Helixi109 – 13123Combined sources
Helixi143 – 1508Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Xmodel-O66-130[»]
1S1Helectron microscopy11.70O66-130[»]
1VW9electron microscopy6.10O1-151[»]
1VWVelectron microscopy6.10O1-151[»]
1VXWelectron microscopy6.20N1-151[»]
1VXZelectron microscopy6.30N1-151[»]
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.
InParanoidiP05756.
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

        10         20         30         40         50
MGRMHSAGKG ISSSAIPYSR NAPAWFKLSS ESVIEQIVKY ARKGLTPSQI
60 70 80 90 100
GVLLRDAHGV TQARVITGNK IMRILKSNGL APEIPEDLYY LIKKAVSVRK
110 120 130 140 150
HLERNRKDKD AKFRLILIES RIHRLARYYR TVAVLPPNWK YESATASALV

N
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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 [» ]
1VXW electron microscopy 6.20 N 1-151 [» ]
1VXZ electron microscopy 6.30 N 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. 149 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.
InParanoidi P05756.
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.
REACT_232946. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_248935. Ribosomal scanning and start codon recognition.
REACT_252688. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_257608. Formation of the ternary complex, and subsequently, the 43S complex.
REACT_257951. Peptide chain elongation.

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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 141 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