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Protein

40S ribosomal protein S3

Gene

RPS3

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

GO - Molecular functioni

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • DNA repair Source: GO_Central
  • ribosomal small subunit export from nucleus Source: SGD
  • 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.
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 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
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL178W.
SGDiS000005122. RPS3.

Subcellular locationi

GO - Cellular componenti

  • cytosolic small ribosomal subunit Source: SGD
  • nucleus Source: GO_Central
  • preribosome, small subunit precursor Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved3 Publications
ChainiPRO_00001303322 – 24040S ribosomal protein S3Add BLAST239

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei44PhosphothreonineCombined sources1
Modified residuei70PhosphothreonineCombined sources1
Modified residuei97PhosphoserineCombined sources1
Cross-linki106Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei129PhosphoserineCombined sources1
Cross-linki132Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki141Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei146Omega-N-methylarginine; by SFM11 Publication1
Cross-linki151Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki200Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki212Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources1 Publication
Modified residuei221PhosphoserineCombined sources1
Modified residuei231PhosphothreonineCombined sources1

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP05750.
PRIDEiP05750.

2D gel databases

UCD-2DPAGEP05750.

PTM databases

iPTMnetiP05750.

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

Binary interactionsi

WithEntry#Exp.IntActNotes
YAR1P466832EBI-16140,EBI-20829

Protein-protein interaction databases

BioGridi35653. 93 interactors.
DIPiDIP-4328N.
IntActiP05750. 101 interactors.
MINTiMINT-512497.

Structurei

Secondary structure

1240
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi15 – 28Combined sources14
Turni29 – 33Combined sources5
Beta strandi34 – 42Combined sources9
Beta strandi45 – 53Combined sources9
Helixi55 – 59Combined sources5
Helixi64 – 77Combined sources14
Beta strandi83 – 90Combined sources8
Helixi94 – 96Combined sources3
Helixi98 – 110Combined sources13
Helixi115 – 128Combined sources14
Beta strandi134 – 141Combined sources8
Beta strandi152 – 159Combined sources8
Helixi163 – 167Combined sources5
Beta strandi168 – 176Combined sources9
Beta strandi181 – 189Combined sources9
Helixi192 – 194Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K5Xmodel-C6-193[»]
3J6Xelectron microscopy6.10S31-240[»]
3J6Yelectron microscopy6.10S31-240[»]
3J77electron microscopy6.20S31-240[»]
3J78electron microscopy6.30S31-240[»]
3V88X-ray3.00D1-240[»]
4BSZX-ray2.84A1-240[»]
4U3MX-ray3.00S3/s32-240[»]
4U3NX-ray3.20S3/s32-240[»]
4U3UX-ray2.90S3/s32-240[»]
4U4NX-ray3.10S3/s32-240[»]
4U4OX-ray3.60S3/s32-240[»]
4U4QX-ray3.00S3/s32-240[»]
4U4RX-ray2.80S3/s32-240[»]
4U4UX-ray3.00S3/s32-240[»]
4U4YX-ray3.20S3/s32-240[»]
4U4ZX-ray3.10S3/s32-240[»]
4U50X-ray3.20S3/s32-240[»]
4U51X-ray3.20S3/s32-240[»]
4U52X-ray3.00S3/s32-240[»]
4U53X-ray3.30S3/s32-240[»]
4U55X-ray3.20S3/s32-240[»]
4U56X-ray3.45S3/s32-240[»]
4U6FX-ray3.10S3/s32-240[»]
4V4Belectron microscopy11.70AC2-193[»]
4V6Ielectron microscopy8.80AB1-240[»]
4V7RX-ray4.00AC/CC1-240[»]
4V88X-ray3.00AD/CD1-240[»]
4V8Yelectron microscopy4.30AD1-240[»]
4V8Zelectron microscopy6.60AD1-240[»]
4V92electron microscopy3.70D4-225[»]
5DATX-ray3.15S3/s32-240[»]
5DC3X-ray3.25S3/s32-240[»]
5FCIX-ray3.40S3/s32-240[»]
5FCJX-ray3.10S3/s32-240[»]
5I4LX-ray3.10S3/s33-225[»]
5JUOelectron microscopy4.00AB1-240[»]
5JUPelectron microscopy3.50AB1-240[»]
5JUSelectron microscopy4.20AB1-240[»]
5JUTelectron microscopy4.00AB1-240[»]
5JUUelectron microscopy4.00AB1-240[»]
ProteinModelPortaliP05750.
SMRiP05750.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05750.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini21 – 92KH type-2PROSITE-ProRule annotationAdd BLAST72

Sequence similaritiesi

Belongs to the ribosomal protein S3P family.Curated
Contains 1 KH type-2 domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000008610.
HOGENOMiHOG000210611.
InParanoidiP05750.
KOiK02985.
OMAiKVKIMRA.
OrthoDBiEOG092C4AZQ.

Family and domain databases

Gene3Di3.30.1140.32. 1 hit.
3.30.300.20. 1 hit.
InterProiIPR015946. KH_dom-like_a/b.
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.
[Graphical view]
SUPFAMiSSF54814. SSF54814. 1 hit.
SSF54821. SSF54821. 1 hit.
TIGRFAMsiTIGR01008. uS3_euk_arch. 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

        10         20         30         40         50
MVALISKKRK LVADGVFYAE LNEFFTRELA EEGYSGVEVR VTPTKTEVII
60 70 80 90 100
RATRTQDVLG ENGRRINELT LLVQKRFKYA PGTIVLYAER VQDRGLSAVA
110 120 130 140 150
QAESMKFKLL NGLAIRRAAY GVVRYVMESG AKGCEVVVSG KLRAARAKAM
160 170 180 190 200
KFADGFLIHS GQPVNDFIDT ATRHVLMRQG VLGIKVKIMR DPAKSRTGPK
210 220 230 240
ALPDAVTIIE PKEEEPILAP SVKDYRPAEE TEAQAEPVEA
Length:240
Mass (Da):26,503
Last modified:January 23, 2007 - v5
Checksum:iB85C0DFEB011745F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti17F → N in AAA35010 (Ref. 3) Curated1
Sequence conflicti223 – 224KD → NH in AAA35010 (Ref. 3) Curated2

Mass spectrometryi

Molecular mass is 26384.3 Da from positions 2 - 240. Determined by ESI. The measured mass is that of the monomethylated protein.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K5Xmodel-C6-193[»]
3J6Xelectron microscopy6.10S31-240[»]
3J6Yelectron microscopy6.10S31-240[»]
3J77electron microscopy6.20S31-240[»]
3J78electron microscopy6.30S31-240[»]
3V88X-ray3.00D1-240[»]
4BSZX-ray2.84A1-240[»]
4U3MX-ray3.00S3/s32-240[»]
4U3NX-ray3.20S3/s32-240[»]
4U3UX-ray2.90S3/s32-240[»]
4U4NX-ray3.10S3/s32-240[»]
4U4OX-ray3.60S3/s32-240[»]
4U4QX-ray3.00S3/s32-240[»]
4U4RX-ray2.80S3/s32-240[»]
4U4UX-ray3.00S3/s32-240[»]
4U4YX-ray3.20S3/s32-240[»]
4U4ZX-ray3.10S3/s32-240[»]
4U50X-ray3.20S3/s32-240[»]
4U51X-ray3.20S3/s32-240[»]
4U52X-ray3.00S3/s32-240[»]
4U53X-ray3.30S3/s32-240[»]
4U55X-ray3.20S3/s32-240[»]
4U56X-ray3.45S3/s32-240[»]
4U6FX-ray3.10S3/s32-240[»]
4V4Belectron microscopy11.70AC2-193[»]
4V6Ielectron microscopy8.80AB1-240[»]
4V7RX-ray4.00AC/CC1-240[»]
4V88X-ray3.00AD/CD1-240[»]
4V8Yelectron microscopy4.30AD1-240[»]
4V8Zelectron microscopy6.60AD1-240[»]
4V92electron microscopy3.70D4-225[»]
5DATX-ray3.15S3/s32-240[»]
5DC3X-ray3.25S3/s32-240[»]
5FCIX-ray3.40S3/s32-240[»]
5FCJX-ray3.10S3/s32-240[»]
5I4LX-ray3.10S3/s33-225[»]
5JUOelectron microscopy4.00AB1-240[»]
5JUPelectron microscopy3.50AB1-240[»]
5JUSelectron microscopy4.20AB1-240[»]
5JUTelectron microscopy4.00AB1-240[»]
5JUUelectron microscopy4.00AB1-240[»]
ProteinModelPortaliP05750.
SMRiP05750.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35653. 93 interactors.
DIPiDIP-4328N.
IntActiP05750. 101 interactors.
MINTiMINT-512497.

PTM databases

iPTMnetiP05750.

2D gel databases

UCD-2DPAGEP05750.

Proteomic databases

MaxQBiP05750.
PRIDEiP05750.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL178W; YNL178W; YNL178W.
GeneIDi855543.
KEGGisce:YNL178W.

Organism-specific databases

EuPathDBiFungiDB:YNL178W.
SGDiS000005122. RPS3.

Phylogenomic databases

GeneTreeiENSGT00390000008610.
HOGENOMiHOG000210611.
InParanoidiP05750.
KOiK02985.
OMAiKVKIMRA.
OrthoDBiEOG092C4AZQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-33190-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

EvolutionaryTraceiP05750.
PROiP05750.

Family and domain databases

Gene3Di3.30.1140.32. 1 hit.
3.30.300.20. 1 hit.
InterProiIPR015946. KH_dom-like_a/b.
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.
[Graphical view]
SUPFAMiSSF54814. SSF54814. 1 hit.
SSF54821. SSF54821. 1 hit.
TIGRFAMsiTIGR01008. uS3_euk_arch. 1 hit.
PROSITEiPS50823. KH_TYPE_2. 1 hit.
PS00548. RIBOSOMAL_S3. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 181 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.1 Publication

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

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.