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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: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

  • small ribosomal subunit 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
  • translation Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-29671-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
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 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
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR064W.
SGDiS000002471. RPS13.

Subcellular locationi

GO - Cellular componenti

  • cytosolic small ribosomal subunit Source: SGD
  • nucleolus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00001156892 – 15140S ribosomal protein S13Add BLAST150

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei32PhosphoserineCombined sources1
Cross-linki39Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki43Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP05756.
PRIDEiP05756.
TopDownProteomicsiP05756.

PTM databases

iPTMnetiP05756.

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. 65 interactors.
IntActiP05756. 55 interactors.
MINTiMINT-8285180.

Structurei

Secondary structure

1151
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 7Combined sources4
Helixi30 – 42Combined sources13
Helixi47 – 56Combined sources10
Turni57 – 59Combined sources3
Helixi63 – 66Combined sources4
Beta strandi67 – 69Combined sources3
Helixi71 – 77Combined sources7
Helixi86 – 104Combined sources19
Turni105 – 107Combined sources3
Helixi109 – 131Combined sources23
Helixi143 – 150Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K5Xmodel-O66-130[»]
3J6Xelectron microscopy6.10131-151[»]
3J6Yelectron microscopy6.10131-151[»]
3J77electron microscopy6.20131-151[»]
3J78electron microscopy6.30131-151[»]
3V88X-ray3.00N1-151[»]
4U3MX-ray3.00C3/c32-151[»]
4U3NX-ray3.20C3/c32-151[»]
4U3UX-ray2.90C3/c32-151[»]
4U4NX-ray3.10C3/c32-151[»]
4U4OX-ray3.60C3/c32-151[»]
4U4QX-ray3.00C3/c32-151[»]
4U4RX-ray2.80C3/c32-151[»]
4U4UX-ray3.00C3/c32-151[»]
4U4YX-ray3.20C3/c32-151[»]
4U4ZX-ray3.10C3/c32-151[»]
4U50X-ray3.20C3/c32-151[»]
4U51X-ray3.20C3/c32-151[»]
4U52X-ray3.00C3/c32-151[»]
4U53X-ray3.30C3/c32-151[»]
4U55X-ray3.20C3/c32-151[»]
4U56X-ray3.45C3/c32-151[»]
4U6FX-ray3.10C3/c32-151[»]
4V4Belectron microscopy11.70AO66-130[»]
4V6Ielectron microscopy8.80AO1-151[»]
4V7RX-ray4.00AG/CG1-151[»]
4V88X-ray3.00AN/CN1-151[»]
4V8Yelectron microscopy4.30AN1-151[»]
4V8Zelectron microscopy6.60AN1-151[»]
4V92electron microscopy3.70N2-151[»]
5DATX-ray3.15C3/c32-151[»]
5DC3X-ray3.25C3/c32-151[»]
5FCIX-ray3.40C3/c32-151[»]
5FCJX-ray3.10C3/c32-151[»]
5I4LX-ray3.10C3/c32-151[»]
5JPQelectron microscopy7.30v1-151[»]
5JUOelectron microscopy4.00KB1-151[»]
5JUPelectron microscopy3.50KB1-151[»]
5JUSelectron microscopy4.20KB1-151[»]
5JUTelectron microscopy4.00KB1-151[»]
5JUUelectron microscopy4.00KB1-151[»]
ProteinModelPortaliP05756.
SMRiP05756.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05756.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein S15P family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000017491.
HOGENOMiHOG000180723.
InParanoidiP05756.
KOiK02953.
OMAiYSRNAPS.
OrthoDBiEOG092C5Q82.

Family and domain databases

CDDicd00353. Ribosomal_S15p_S13e. 1 hit.
HAMAPiMF_01343_A. Ribosomal_S15_A. 1 hit.
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]
SMARTiSM01386. Ribosomal_S13_N. 1 hit.
SM01387. 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)DescriptionActionsGraphical viewLength
Sequence conflicti25W → G AA sequence (PubMed:6814480).Curated1
Sequence conflicti32S → C AA sequence (PubMed:6814480).Curated1

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.
PIRiS54048.
RefSeqiNP_010349.3. NM_001180372.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K5Xmodel-O66-130[»]
3J6Xelectron microscopy6.10131-151[»]
3J6Yelectron microscopy6.10131-151[»]
3J77electron microscopy6.20131-151[»]
3J78electron microscopy6.30131-151[»]
3V88X-ray3.00N1-151[»]
4U3MX-ray3.00C3/c32-151[»]
4U3NX-ray3.20C3/c32-151[»]
4U3UX-ray2.90C3/c32-151[»]
4U4NX-ray3.10C3/c32-151[»]
4U4OX-ray3.60C3/c32-151[»]
4U4QX-ray3.00C3/c32-151[»]
4U4RX-ray2.80C3/c32-151[»]
4U4UX-ray3.00C3/c32-151[»]
4U4YX-ray3.20C3/c32-151[»]
4U4ZX-ray3.10C3/c32-151[»]
4U50X-ray3.20C3/c32-151[»]
4U51X-ray3.20C3/c32-151[»]
4U52X-ray3.00C3/c32-151[»]
4U53X-ray3.30C3/c32-151[»]
4U55X-ray3.20C3/c32-151[»]
4U56X-ray3.45C3/c32-151[»]
4U6FX-ray3.10C3/c32-151[»]
4V4Belectron microscopy11.70AO66-130[»]
4V6Ielectron microscopy8.80AO1-151[»]
4V7RX-ray4.00AG/CG1-151[»]
4V88X-ray3.00AN/CN1-151[»]
4V8Yelectron microscopy4.30AN1-151[»]
4V8Zelectron microscopy6.60AN1-151[»]
4V92electron microscopy3.70N2-151[»]
5DATX-ray3.15C3/c32-151[»]
5DC3X-ray3.25C3/c32-151[»]
5FCIX-ray3.40C3/c32-151[»]
5FCJX-ray3.10C3/c32-151[»]
5I4LX-ray3.10C3/c32-151[»]
5JPQelectron microscopy7.30v1-151[»]
5JUOelectron microscopy4.00KB1-151[»]
5JUPelectron microscopy3.50KB1-151[»]
5JUSelectron microscopy4.20KB1-151[»]
5JUTelectron microscopy4.00KB1-151[»]
5JUUelectron microscopy4.00KB1-151[»]
ProteinModelPortaliP05756.
SMRiP05756.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32119. 65 interactors.
IntActiP05756. 55 interactors.
MINTiMINT-8285180.

PTM databases

iPTMnetiP05756.

Proteomic databases

MaxQBiP05756.
PRIDEiP05756.
TopDownProteomicsiP05756.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YDR064W.
SGDiS000002471. RPS13.

Phylogenomic databases

GeneTreeiENSGT00390000017491.
HOGENOMiHOG000180723.
InParanoidiP05756.
KOiK02953.
OMAiYSRNAPS.
OrthoDBiEOG092C5Q82.

Enzyme and pathway databases

BioCyciYEAST:G3O-29671-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
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

EvolutionaryTraceiP05756.
PROiP05756.

Family and domain databases

CDDicd00353. Ribosomal_S15p_S13e. 1 hit.
HAMAPiMF_01343_A. Ribosomal_S15_A. 1 hit.
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]
SMARTiSM01386. Ribosomal_S13_N. 1 hit.
SM01387. Ribosomal_S15. 1 hit.
[Graphical view]
SUPFAMiSSF47060. SSF47060. 1 hit.
PROSITEiPS00362. RIBOSOMAL_S15. 1 hit.
[Graphical view]
ProtoNetiSearch...

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 30, 2016
This is version 163 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

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.