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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

Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel.1 Publication

Miscellaneous

Present with 146000 molecules/cell in log phase SD medium.1 Publication

GO - Molecular functioni

GO - Biological processi

  • cytoplasmic translation Source: GO_Central
  • DNA repair Source: GO_Central
  • ribosomal small subunit export from nucleus Source: SGD
  • rRNA export from nucleus Source: SGD

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein, 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 S31 Publication
Alternative name(s):
RP13
Small ribosomal subunit protein uS31 Publication
YS3
Gene namesi
Name:RPS31 Publication
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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 sources
Modified residuei221PhosphoserineCombined sources1
Modified residuei231PhosphothreonineCombined sources1

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP05750.
PRIDEiP05750.

2D gel databases

UCD-2DPAGEiP05750.

PTM databases

iPTMnetiP05750.

Interactioni

Subunit structurei

Component of the small ribosomal subunit (SSU). Mature yeast ribosomes consist of a small (40S) and a large (60S) subunit. The 40S small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes) (PubMed:9559554, PubMed:22096102).1 Publication1 Publication

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi35653. 275 interactors.
DIPiDIP-4328N.
IntActiP05750. 104 interactors.
MINTiMINT-512497.
STRINGi4932.YNL178W.

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[»]
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[»]
5DGEX-ray3.45S3/s32-240[»]
5DGFX-ray3.30S3/s32-240[»]
5DGVX-ray3.10S3/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[»]
5LYBX-ray3.25S3/s33-225[»]
5M1Jelectron microscopy3.30D23-225[»]
5MC6electron microscopy3.80A1-240[»]
5MEIX-ray3.50E/s33-225[»]
5TBWX-ray3.00E/s33-225[»]
5TGAX-ray3.30S3/s33-225[»]
5TGMX-ray3.50S3/s33-225[»]
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

Phylogenomic databases

GeneTreeiENSGT00390000008610.
HOGENOMiHOG000210611.
InParanoidiP05750.
KOiK02985.
OMAiDHATRHV.
OrthoDBiEOG092C4AZQ.

Family and domain databases

Gene3Di3.30.1140.32. 1 hit.
3.30.300.20. 1 hit.
InterProiView protein in InterPro
IPR015946. KH_dom-like_a/b.
IPR004044. KH_dom_type_2.
IPR009019. KH_prok-type.
IPR001351. Ribosomal_S3_C.
IPR036419. Ribosomal_S3_C_sf.
IPR018280. Ribosomal_S3_CS.
IPR005703. Ribosomal_S3_euk/arc.
PfamiView protein in Pfam
PF07650. KH_2. 1 hit.
PF00189. Ribosomal_S3_C. 1 hit.
SUPFAMiSSF54814. SSF54814. 1 hit.
SSF54821. SSF54821. 1 hit.
TIGRFAMsiTIGR01008. uS3_euk_arch. 1 hit.
PROSITEiView protein in PROSITE
PS50823. KH_TYPE_2. 1 hit.
PS00548. RIBOSOMAL_S3. 1 hit.

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

P05750: 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.

Similar proteinsi

Entry informationi

Entry nameiRS3_YEAST
AccessioniPrimary (citable) accession number: P05750
Secondary accession number(s): D6W107
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: January 23, 2007
Last modified: October 25, 2017
This is version 190 of the entry and version 5 of the sequence. See 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names