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Protein

60S ribosomal protein L13-B

Gene

RPL13B

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

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 54200 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for eL13 in yeast.Curated

GO - Molecular functioni

  • RNA binding Source: GO_Central
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • macroautophagy Source: SGD
  • translation Source: GO_Central

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-32834-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-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:
60S ribosomal protein L13-B1 Publication
Alternative name(s):
Large ribosomal subunit protein eL13-B1 Publication
Gene namesi
Name:RPL13B1 Publication
Synonyms:RPL13
Ordered Locus Names:YMR142C
ORF Names:YM9375.11C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR142C.
SGDiS000004750. RPL13B.

Subcellular locationi

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: SGD

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001929391 – 19960S ribosomal protein L13-BAdd BLAST199

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei144PhosphothreonineCombined sources1
Modified residuei152PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP40212.
PRIDEiP40212.
TopDownProteomicsiP40212.

PTM databases

iPTMnetiP40212.

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

Protein-protein interaction databases

BioGridi35318. 65 interactors.
DIPiDIP-2591N.
IntActiP40212. 61 interactors.
MINTiMINT-8285395.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4V91electron microscopy3.70L1-199[»]
ProteinModelPortaliP40212.
SMRiP40212.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000007818.
HOGENOMiHOG000170452.
InParanoidiP40212.
KOiK02873.
OMAiAHITRDS.
OrthoDBiEOG092C53VP.

Family and domain databases

InterProiView protein in InterPro
IPR034295. Ribosomal_L13_euk.
IPR001380. Ribosomal_L13e.
IPR018256. Ribosomal_L13e_CS.
PANTHERiPTHR11722. PTHR11722. 1 hit.
PfamiView protein in Pfam
PF01294. Ribosomal_L13e. 1 hit.
PROSITEiView protein in PROSITE
PS01104. RIBOSOMAL_L13E. 1 hit.

Sequencei

Sequence statusi: Complete.

P40212-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAISKNLPIL KNHFRKHWQE RVKVHFDQAG KKVSRRNARA ARAAKIAPRP
60 70 80 90 100
LDLLRPVVRA PTVKYNRKVR AGRGFTLAEV KAAGLTAAYA RTIGIAVDHR
110 120 130 140 150
RQNRNQEIFD ANVQRLKEYQ SKIIVFPRDG KAPEAEQVLS AAATFPIAQP
160 170 180 190
ATDVEARAVQ DNGESAFRTL RLARSEKKFR GIREKRAREK AEAEAEKKK
Length:199
Mass (Da):22,525
Last modified:February 1, 1995 - v1
Checksum:iBEA3B423EE76EF23
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z47071 Genomic DNA. Translation: CAA87356.1.
BK006946 Genomic DNA. Translation: DAA10038.1.
PIRiS50398.
RefSeqiNP_013862.1. NM_001182644.1.

Genome annotation databases

EnsemblFungiiYMR142C; YMR142C; YMR142C.
GeneIDi855173.
KEGGisce:YMR142C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z47071 Genomic DNA. Translation: CAA87356.1.
BK006946 Genomic DNA. Translation: DAA10038.1.
PIRiS50398.
RefSeqiNP_013862.1. NM_001182644.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4V91electron microscopy3.70L1-199[»]
ProteinModelPortaliP40212.
SMRiP40212.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35318. 65 interactors.
DIPiDIP-2591N.
IntActiP40212. 61 interactors.
MINTiMINT-8285395.

PTM databases

iPTMnetiP40212.

Proteomic databases

MaxQBiP40212.
PRIDEiP40212.
TopDownProteomicsiP40212.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR142C; YMR142C; YMR142C.
GeneIDi855173.
KEGGisce:YMR142C.

Organism-specific databases

EuPathDBiFungiDB:YMR142C.
SGDiS000004750. RPL13B.

Phylogenomic databases

GeneTreeiENSGT00390000007818.
HOGENOMiHOG000170452.
InParanoidiP40212.
KOiK02873.
OMAiAHITRDS.
OrthoDBiEOG092C53VP.

Enzyme and pathway databases

BioCyciYEAST:G3O-32834-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-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

PROiPR:P40212.

Family and domain databases

InterProiView protein in InterPro
IPR034295. Ribosomal_L13_euk.
IPR001380. Ribosomal_L13e.
IPR018256. Ribosomal_L13e_CS.
PANTHERiPTHR11722. PTHR11722. 1 hit.
PfamiView protein in Pfam
PF01294. Ribosomal_L13e. 1 hit.
PROSITEiView protein in PROSITE
PS01104. RIBOSOMAL_L13E. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRL13B_YEAST
AccessioniPrimary (citable) accession number: P40212
Secondary accession number(s): D6VZW4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: April 12, 2017
This is version 129 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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 XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: 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.