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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)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved3 Publications
Chaini2 – 24023940S ribosomal protein S3PRO_0000130332Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei44 – 441PhosphothreonineCombined sources
Modified residuei70 – 701PhosphothreonineCombined sources
Modified residuei97 – 971PhosphoserineCombined sources
Cross-linki106 – 106Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei129 – 1291PhosphoserineCombined sources
Cross-linki132 – 132Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki141 – 141Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei146 – 1461Omega-N-methylarginine; by SFM11 Publication
Cross-linki151 – 151Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki200 – 200Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki212 – 212Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources1 Publication
Modified residuei221 – 2211PhosphoserineCombined sources
Modified residuei231 – 2311PhosphothreonineCombined sources

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 interactions.
DIPiDIP-4328N.
IntActiP05750. 101 interactions.
MINTiMINT-512497.

Structurei

Secondary structure

1
240
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi15 – 2814Combined sources
Turni29 – 335Combined sources
Beta strandi34 – 429Combined sources
Beta strandi45 – 539Combined sources
Helixi55 – 595Combined sources
Helixi64 – 7714Combined sources
Beta strandi83 – 908Combined sources
Helixi94 – 963Combined sources
Helixi98 – 11013Combined sources
Helixi115 – 12814Combined sources
Beta strandi134 – 1418Combined sources
Beta strandi152 – 1598Combined sources
Helixi163 – 1675Combined sources
Beta strandi168 – 1769Combined sources
Beta strandi181 – 1899Combined sources
Helixi192 – 1943Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
5DC3X-ray3.25S3/s32-240[»]
5FCIX-ray3.40S3/s32-240[»]
5FCJX-ray3.10S3/s32-240[»]
5I4LX-ray3.10S3/s33-225[»]
ProteinModelPortaliP05750.
SMRiP05750. Positions 3-225.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05750.

Family & Domainsi

Domains and Repeats

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

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.
InterProiIPR004044. 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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti17 – 171F → N in AAA35010 (Ref. 3) Curated
Sequence conflicti223 – 2242KD → NH in AAA35010 (Ref. 3) Curated

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
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[»]
5DC3X-ray3.25S3/s32-240[»]
5FCIX-ray3.40S3/s32-240[»]
5FCJX-ray3.10S3/s32-240[»]
5I4LX-ray3.10S3/s33-225[»]
ProteinModelPortaliP05750.
SMRiP05750. Positions 3-225.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35653. 93 interactions.
DIPiDIP-4328N.
IntActiP05750. 101 interactions.
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.
InterProiIPR004044. 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: September 7, 2016
This is version 178 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.