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P05750

- RS3_YEAST

UniProt

P05750 - RS3_YEAST

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Protein

40S ribosomal protein S3

Gene
RPS3, SUF14, YNL178W, N1653
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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
Complete GO annotation...

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.

Miscellaneous databases

EvolutionaryTraceiP05750.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Contains 1 KH type-2 domain.

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

Sequence conflict

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

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 156 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.

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

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