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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

  • rRNA binding Source: SGD
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • positive regulation of translational fidelity Source: GO_Central
  • rRNA methylation Source: Reactome
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.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-SCE-6790901. rRNA modification in the nucleus and cytosol.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.
R-SCE-72689. Formation of a pool of free 40S subunits.
R-SCE-72695. Formation of the ternary complex, and subsequently, the 43S complex.
R-SCE-72702. Ribosomal scanning and start codon recognition.
R-SCE-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

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
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL081W.
SGDiS000006002. RPS9A.

Subcellular locationi

GO - Cellular componenti

  • cytosolic small ribosomal subunit Source: SGD
  • nucleolus Source: UniProtKB-SubCell
  • nucleoplasm Source: Reactome
  • small-subunit processome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001327032 – 19740S ribosomal protein S9-AAdd BLAST196

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki180Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei184PhosphoserineBy similarity1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiO13516.
PRIDEiO13516.
TopDownProteomicsiO13516.

PTM databases

iPTMnetiO13516.

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. 53 interactors.
IntActiO13516. 29 interactors.
MINTiMINT-2786178.

Structurei

Secondary structure

1197
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi16 – 18Combined sources3
Helixi21 – 34Combined sources14
Beta strandi37 – 39Combined sources3
Helixi40 – 61Combined sources22
Helixi67 – 82Combined sources16
Beta strandi84 – 86Combined sources3
Beta strandi88 – 90Combined sources3
Turni94 – 96Combined sources3
Helixi101 – 105Combined sources5
Helixi109 – 115Combined sources7
Beta strandi116 – 118Combined sources3
Helixi122 – 130Combined sources9
Beta strandi135 – 138Combined sources4
Helixi150 – 155Combined sources6
Beta strandi156 – 158Combined sources3
Beta strandi160 – 167Combined sources8
Helixi171 – 180Combined sources10
Turni181 – 183Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5DATX-ray3.15S9/s92-197[»]
5DC3X-ray3.25S9/s92-197[»]
5FCIX-ray3.40S9/s92-197[»]
5FCJX-ray3.10S9/s92-197[»]
5I4LX-ray3.10S9/s92-186[»]
5JPQelectron microscopy7.30u1-197[»]
5JUOelectron microscopy4.00GB1-197[»]
5JUPelectron microscopy3.50GB1-197[»]
5JUSelectron microscopy4.20GB1-197[»]
5JUTelectron microscopy4.00GB1-197[»]
5JUUelectron microscopy4.00GB1-197[»]
ProteinModelPortaliO13516.
SMRiO13516.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO13516.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 181S4 RNA-bindingPROSITE-ProRule annotationAdd BLAST75

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.
OMAiHIDFAHN.
OrthoDBiEOG092C4UYC.

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.
PfamiPF01479. S4. 1 hit.
[Graphical view]
SMARTiSM01390. Ribosomal_S4. 1 hit.
SM00363. S4. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01018. uS4_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)DescriptionActionsGraphical viewLength
Sequence conflicti20 – 22ESS → QSB AA sequence (PubMed:6814480).Curated3

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
PDB 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[»]
5DATX-ray3.15S9/s92-197[»]
5DC3X-ray3.25S9/s92-197[»]
5FCIX-ray3.40S9/s92-197[»]
5FCJX-ray3.10S9/s92-197[»]
5I4LX-ray3.10S9/s92-186[»]
5JPQelectron microscopy7.30u1-197[»]
5JUOelectron microscopy4.00GB1-197[»]
5JUPelectron microscopy3.50GB1-197[»]
5JUSelectron microscopy4.20GB1-197[»]
5JUTelectron microscopy4.00GB1-197[»]
5JUUelectron microscopy4.00GB1-197[»]
ProteinModelPortaliO13516.
SMRiO13516.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36100. 53 interactors.
IntActiO13516. 29 interactors.
MINTiMINT-2786178.

PTM databases

iPTMnetiO13516.

Proteomic databases

MaxQBiO13516.
PRIDEiO13516.
TopDownProteomicsiO13516.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YPL081W.
SGDiS000006002. RPS9A.

Phylogenomic databases

GeneTreeiENSGT00550000074829.
HOGENOMiHOG000194525.
InParanoidiO13516.
KOiK02997.
OMAiHIDFAHN.
OrthoDBiEOG092C4UYC.

Enzyme and pathway databases

BioCyciYEAST:G3O-33987-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-SCE-6790901. rRNA modification in the nucleus and cytosol.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.
R-SCE-72689. Formation of a pool of free 40S subunits.
R-SCE-72695. Formation of the ternary complex, and subsequently, the 43S complex.
R-SCE-72702. Ribosomal scanning and start codon recognition.
R-SCE-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

EvolutionaryTraceiO13516.
PROiO13516.

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.
PfamiPF01479. S4. 1 hit.
[Graphical view]
SMARTiSM01390. Ribosomal_S4. 1 hit.
SM00363. S4. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01018. uS4_arch. 1 hit.
PROSITEiPS00632. RIBOSOMAL_S4. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 154 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

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 one 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.