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Protein

40S ribosomal protein S9-A

Gene

RPS9A

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

Functioni

Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.1 Publication

GO - Molecular functioni

  1. 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

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33987-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_335938. Ribosomal scanning and start codon recognition.
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_351622. Formation of the ternary complex, and subsequently, the 43S complex.

Names & Taxonomyi

Protein namesi
Recommended name:
40S ribosomal protein S9-A
Alternative name(s):
RP21
S13
YP28
YS11
Gene namesi
Name:RPS9A
Synonyms:RPS13A, YS11A
Ordered Locus Names:YPL081W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XVI

Organism-specific databases

SGDiS000006002. RPS9A.

Subcellular locationi

GO - Cellular componenti

  1. cytosolic small ribosomal subunit Source: SGD
  2. nucleolus Source: UniProtKB-SubCell
  3. small-subunit processome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 19719640S ribosomal protein S9-APRO_0000132703Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei184 – 1841PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO13516.
PeptideAtlasiO13516.
PRIDEiO13516.

Expressioni

Gene expression databases

GenevestigatoriO13516.

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). Interacts with snoRNA U3. Interacts with MPP10. Component of the ribosomal small subunit (SSU) processome composed of at least 40 protein subunits and snoRNA U3.2 Publications

Protein-protein interaction databases

BioGridi36100. 62 interactions.
IntActiO13516. 27 interactions.
MINTiMINT-2786178.
STRINGi4932.YPL081W.

Structurei

Secondary structure

1
197
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi16 – 183Combined sources
Helixi21 – 3414Combined sources
Beta strandi37 – 393Combined sources
Helixi40 – 6122Combined sources
Helixi67 – 8216Combined sources
Beta strandi84 – 863Combined sources
Beta strandi88 – 903Combined sources
Turni94 – 963Combined sources
Helixi101 – 1055Combined sources
Helixi109 – 1157Combined sources
Beta strandi116 – 1183Combined sources
Helixi122 – 1309Combined sources
Beta strandi135 – 1384Combined sources
Helixi150 – 1556Combined sources
Beta strandi156 – 1583Combined sources
Beta strandi160 – 1678Combined sources
Helixi171 – 18010Combined sources
Turni181 – 1833Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Xmodel-D19-196[»]
3J6Xelectron microscopy6.10S91-197[»]
3J6Yelectron microscopy6.10S91-197[»]
3J77electron microscopy6.20S91-197[»]
3J78electron microscopy6.30S91-197[»]
3V88X-ray3.00J1-197[»]
4U3MX-ray3.00S9/s92-197[»]
4U3NX-ray3.20S9/s92-197[»]
4U3UX-ray2.90S9/s92-197[»]
4U4NX-ray3.10S9/s92-197[»]
4U4OX-ray3.60S9/s92-197[»]
4U4QX-ray3.00S9/s92-197[»]
4U4RX-ray2.80S9/s92-197[»]
4U4UX-ray3.00S9/s92-197[»]
4U4YX-ray3.20S9/s92-197[»]
4U4ZX-ray3.10S9/s92-197[»]
4U50X-ray3.20S9/s92-197[»]
4U51X-ray3.20S9/s92-197[»]
4U52X-ray3.00S9/s92-197[»]
4U53X-ray3.30S9/s92-197[»]
4U55X-ray3.20S9/s92-197[»]
4U56X-ray3.45S9/s92-197[»]
4U6FX-ray3.10S9/s92-197[»]
4V4Belectron microscopy11.70AD19-197[»]
4V6Ielectron microscopy8.80AC1-197[»]
4V7RX-ray4.00AE/CE1-197[»]
4V88X-ray3.00AJ/CJ1-197[»]
4V8Yelectron microscopy4.30AJ1-197[»]
4V8Zelectron microscopy6.60AJ1-197[»]
4V92electron microscopy3.70J2-180[»]
ProteinModelPortaliO13516.
SMRiO13516. Positions 2-186.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO13516.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 18175S4 RNA-bindingPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ribosomal protein S4P family.Curated
Contains 1 S4 RNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00550000074829.
HOGENOMiHOG000194525.
InParanoidiO13516.
KOiK02997.
OMAiIWRIGLT.
OrthoDBiEOG790GCC.

Family and domain databases

Gene3Di3.10.290.10. 1 hit.
InterProiIPR022801. Ribosomal_S4/S9.
IPR005710. Ribosomal_S4/S9_euk/arc.
IPR001912. Ribosomal_S4/S9_N.
IPR018079. Ribosomal_S4_CS.
IPR002942. S4_RNA-bd.
[Graphical view]
PANTHERiPTHR11831. PTHR11831. 1 hit.
PfamiPF00163. Ribosomal_S4. 1 hit.
PF01479. S4. 1 hit.
[Graphical view]
SMARTiSM00363. S4. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01018. rpsD_arch. 1 hit.
PROSITEiPS00632. RIBOSOMAL_S4. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O13516-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPRAPRTYSK TYSTPKRPYE SSRLDAELKL AGEFGLKNKK EIYRISFQLS
60 70 80 90 100
KIRRAARDLL TRDEKDPKRL FEGNALIRRL VRVGVLSEDK KKLDYVLALK
110 120 130 140 150
VEDFLERRLQ TQVYKLGLAK SVHHARVLIT QRHIAVGKQI VNIPSFMVRL
160 170 180 190
DSEKHIDFAP TSPFGGARPG RVARRNAARK AEASGEAADE ADEADEE
Length:197
Mass (Da):22,443
Last modified:January 23, 2007 - v3
Checksum:iA5A3641D4D7A34F5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti20 – 223ESS → QSB AA sequence (PubMed:6814480).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D00724 Genomic DNA. Translation: BAA00626.1.
U41849 Genomic DNA. Translation: AAB68268.1.
BK006949 Genomic DNA. Translation: DAA11352.1.
PIRiS16822.
RefSeqiNP_015244.1. NM_001183895.1.

Genome annotation databases

EnsemblFungiiYPL081W; YPL081W; YPL081W.
GeneIDi856024.
KEGGisce:YPL081W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D00724 Genomic DNA. Translation: BAA00626.1.
U41849 Genomic DNA. Translation: AAB68268.1.
BK006949 Genomic DNA. Translation: DAA11352.1.
PIRiS16822.
RefSeqiNP_015244.1. NM_001183895.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Xmodel-D19-196[»]
3J6Xelectron microscopy6.10S91-197[»]
3J6Yelectron microscopy6.10S91-197[»]
3J77electron microscopy6.20S91-197[»]
3J78electron microscopy6.30S91-197[»]
3V88X-ray3.00J1-197[»]
4U3MX-ray3.00S9/s92-197[»]
4U3NX-ray3.20S9/s92-197[»]
4U3UX-ray2.90S9/s92-197[»]
4U4NX-ray3.10S9/s92-197[»]
4U4OX-ray3.60S9/s92-197[»]
4U4QX-ray3.00S9/s92-197[»]
4U4RX-ray2.80S9/s92-197[»]
4U4UX-ray3.00S9/s92-197[»]
4U4YX-ray3.20S9/s92-197[»]
4U4ZX-ray3.10S9/s92-197[»]
4U50X-ray3.20S9/s92-197[»]
4U51X-ray3.20S9/s92-197[»]
4U52X-ray3.00S9/s92-197[»]
4U53X-ray3.30S9/s92-197[»]
4U55X-ray3.20S9/s92-197[»]
4U56X-ray3.45S9/s92-197[»]
4U6FX-ray3.10S9/s92-197[»]
4V4Belectron microscopy11.70AD19-197[»]
4V6Ielectron microscopy8.80AC1-197[»]
4V7RX-ray4.00AE/CE1-197[»]
4V88X-ray3.00AJ/CJ1-197[»]
4V8Yelectron microscopy4.30AJ1-197[»]
4V8Zelectron microscopy6.60AJ1-197[»]
4V92electron microscopy3.70J2-180[»]
ProteinModelPortaliO13516.
SMRiO13516. Positions 2-186.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36100. 62 interactions.
IntActiO13516. 27 interactions.
MINTiMINT-2786178.
STRINGi4932.YPL081W.

Proteomic databases

MaxQBiO13516.
PeptideAtlasiO13516.
PRIDEiO13516.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL081W; YPL081W; YPL081W.
GeneIDi856024.
KEGGisce:YPL081W.

Organism-specific databases

SGDiS000006002. RPS9A.

Phylogenomic databases

GeneTreeiENSGT00550000074829.
HOGENOMiHOG000194525.
InParanoidiO13516.
KOiK02997.
OMAiIWRIGLT.
OrthoDBiEOG790GCC.

Enzyme and pathway databases

BioCyciYEAST:G3O-33987-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_335938. Ribosomal scanning and start codon recognition.
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_351622. Formation of the ternary complex, and subsequently, the 43S complex.

Miscellaneous databases

EvolutionaryTraceiO13516.
NextBioi980938.

Gene expression databases

GenevestigatoriO13516.

Family and domain databases

Gene3Di3.10.290.10. 1 hit.
InterProiIPR022801. Ribosomal_S4/S9.
IPR005710. Ribosomal_S4/S9_euk/arc.
IPR001912. Ribosomal_S4/S9_N.
IPR018079. Ribosomal_S4_CS.
IPR002942. S4_RNA-bd.
[Graphical view]
PANTHERiPTHR11831. PTHR11831. 1 hit.
PfamiPF00163. Ribosomal_S4. 1 hit.
PF01479. S4. 1 hit.
[Graphical view]
SMARTiSM00363. S4. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01018. rpsD_arch. 1 hit.
PROSITEiPS00632. RIBOSOMAL_S4. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Yeast ribosomal proteins: XII. YS11 of Saccharomyces cerevisiae is a homologue to E. coli S4 according to the gene analysis."
    Mizuta K., Hashimoto T., Suzuki K., Otaka E.
    Nucleic Acids Res. 19:2603-2608(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1996) [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(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-24.
  5. "The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae."
    Planta R.J., Mager W.H.
    Yeast 14:471-477(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE, SUBUNIT.
  6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "The small-subunit processome is a ribosome assembly intermediate."
    Bernstein K.A., Gallagher J.E.G., Mitchell B.M., Granneman S., Baserga S.J.
    Eukaryot. Cell 3:1619-1626(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH MPP10 AND SNORNA U3, IDENTIFICATION IN SSU PROCESSOME, SUBCELLULAR LOCATION.
  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(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF 19-196, 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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF 19-197, ELECTRON MICROSCOPY.

Entry informationi

Entry nameiRS9A_YEAST
AccessioniPrimary (citable) accession number: O13516
Secondary accession number(s): D6W3T6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 23, 2007
Last modified: April 1, 2015
This is version 137 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 106000 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for S9 in yeast.

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

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.