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Protein

60S ribosomal protein L4-B

Gene

RPL4B

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 151000 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for uL4 in yeast.Curated

GO - Molecular functioni

GO - Biological processi

  • cytoplasmic translation Source: SGD

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein, RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29631-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 L4-B1 Publication
Alternative name(s):
L2
Large ribosomal subunit protein uL4-B1 Publication
RP2
YL2
Gene namesi
Name:RPL4B1 Publication
Synonyms:RPL2B
Ordered Locus Names:YDR012W
ORF Names:YD8119.17
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR012W.
SGDiS000002419. RPL4B.

Subcellular locationi

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: SGD
  • nucleus Source: UniProtKB-SubCell

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi95R → E: Leads to a slower growth at higher temperatures but allows RPL4 assembly into the 60S subunit; when associated with E-98. 1 Publication1
Mutagenesisi98R → E: Leads to a slower growth at higher temperatures but allows RPL4 assembly into the mature 60S; when associated with E-95. 1 Publication1
Mutagenesisi289I → A: Leads to an inefficient release from ACL4 with a delayed assembly into the 60S subunit; when associated with A-290 and A-295. 1 Publication1
Mutagenesisi290I → A: Leads to an inefficient release from ACL4 with a delayed assembly into the 60S subunit; when associated with A-289 and A-295. 1 Publication1
Mutagenesisi295I → A: Leads to an inefficient release from ACL4 with a delayed assembly into the 60S subunit; when associated with A-289 and A-290. 1 Publication1
Mutagenesisi314K → A: Significantly diminished nuclear localization; when associated with A-315 and A-319. 1 Publication1
Mutagenesisi315K → A: Significantly diminished nuclear localization; when associated with A-314 and A-319. 1 Publication1
Mutagenesisi319K → A: Significantly diminished nuclear localization; when associated with A-314 and A-315. 1 Publication1
Mutagenesisi332K → E: Leads to an inefficient release from ACL4 with a delayed assembly into the 60S subunit; when associated with A-334. 1 Publication1
Mutagenesisi334F → A: Leads to an inefficient release from ACL4 with a delayed assembly into the 60S subunit; when associated with e-332. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001293682 – 36260S ribosomal protein L4-BAdd BLAST361

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine1 Publication1

Post-translational modificationi

N-terminally acetylated by acetyltransferase NatA.1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP49626.
PRIDEiP49626.

PTM databases

iPTMnetiP49626.

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). uL4 is associated with the polypeptide exit tunnel (PubMed:9559554, PubMed:22096102). uL4 interacts with its chaperone ACL4 and the nuclear import receptor KAP104 (PubMed:25936803).1 Publication2 Publications

Protein-protein interaction databases

BioGridi32063. 203 interactors.
DIPiDIP-5367N.
IntActiP49626. 209 interactors.
MINTiMINT-8285174.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2WW9electron microscopy8.60H1-362[»]
2WWAelectron microscopy8.90H1-362[»]
2WWBelectron microscopy6.48H1-362[»]
4V4Belectron microscopy11.70BD2-362[»]
ProteinModelPortaliP49626.
SMRiP49626.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP49626.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni277 – 362C-terminal-extended nuclear localization signal1 PublicationAdd BLAST86

Domaini

The eukaryote-specific C-terminal extension harbors a nuclear import signal and delivers the ACL4-uL4/RPL4 complex to the pre-ribosome, triggering uL4 release from ACL4 and incorporation into the 60S ribosomal subunit.1 Publication

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000018145.
HOGENOMiHOG000107331.
InParanoidiP49626.
KOiK02930.
OMAiRSAHPPK.
OrthoDBiEOG092C37AK.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
InterProiView protein in InterPro
IPR025755. Ribos_L4_C_dom.
IPR002136. Ribosomal_L4/L1e.
IPR013000. Ribosomal_L4/L1e_euk/arc_CS.
IPR023574. Ribosomal_L4_dom.
PfamiView protein in Pfam
PF14374. Ribos_L4_asso_C. 1 hit.
PF00573. Ribosomal_L4. 1 hit.
SUPFAMiSSF52166. SSF52166. 1 hit.
PROSITEiView protein in PROSITE
PS00939. RIBOSOMAL_L1E. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P49626-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRPQVTVHS LTGEATANAL PLPAVFSAPI RPDIVHTVFT SVNKNKRQAY
60 70 80 90 100
AVSEKAGHQT SAESWGTGRA VARIPRVGGG GTGRSGQGAF GNMCRGGRMF
110 120 130 140 150
APTKTWRKWN VKVNHNEKRY ATASAIAATA VASLVLARGH RVEKIPEIPL
160 170 180 190 200
VVSTDLESIQ KTKEAVAALK AVGAHSDLLK VLKSKKLRAG KGKYRNRRWT
210 220 230 240 250
QRRGPLVVYA EDNGIVKALR NVPGVETANV ASLNLLQLAP GAHLGRFVIW
260 270 280 290 300
TEAAFTKLDQ VWGSETVASS KVGYTLPSHI ISTSDVTRII NSSEIQSAIR
310 320 330 340 350
PAGQATQKRT HVLKKNPLKN KQVLLRLNPY AKVFAAEKLG SKKAEKTGTK
360
PAAVFAETLK HD
Length:362
Mass (Da):39,062
Last modified:January 23, 2007 - v2
Checksum:i37D0942A10AAF4EF
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti88G → R in AAA34975 (PubMed:3062369).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95966 Genomic DNA. Translation: CAA65204.1.
Z48008 Genomic DNA. Translation: CAA88072.1.
Z74308 Genomic DNA. Translation: CAA98832.1.
AY558570 Genomic DNA. Translation: AAS56896.1.
M22583 Genomic DNA. Translation: AAA34975.1.
BK006938 Genomic DNA. Translation: DAA11858.1.
PIRiS50993.
RefSeqiNP_010295.3. NM_001180320.3.

Genome annotation databases

EnsemblFungiiYDR012W; YDR012W; YDR012W.
GeneIDi851575.
KEGGisce:YDR012W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95966 Genomic DNA. Translation: CAA65204.1.
Z48008 Genomic DNA. Translation: CAA88072.1.
Z74308 Genomic DNA. Translation: CAA98832.1.
AY558570 Genomic DNA. Translation: AAS56896.1.
M22583 Genomic DNA. Translation: AAA34975.1.
BK006938 Genomic DNA. Translation: DAA11858.1.
PIRiS50993.
RefSeqiNP_010295.3. NM_001180320.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2WW9electron microscopy8.60H1-362[»]
2WWAelectron microscopy8.90H1-362[»]
2WWBelectron microscopy6.48H1-362[»]
4V4Belectron microscopy11.70BD2-362[»]
ProteinModelPortaliP49626.
SMRiP49626.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32063. 203 interactors.
DIPiDIP-5367N.
IntActiP49626. 209 interactors.
MINTiMINT-8285174.

PTM databases

iPTMnetiP49626.

Proteomic databases

MaxQBiP49626.
PRIDEiP49626.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR012W; YDR012W; YDR012W.
GeneIDi851575.
KEGGisce:YDR012W.

Organism-specific databases

EuPathDBiFungiDB:YDR012W.
SGDiS000002419. RPL4B.

Phylogenomic databases

GeneTreeiENSGT00390000018145.
HOGENOMiHOG000107331.
InParanoidiP49626.
KOiK02930.
OMAiRSAHPPK.
OrthoDBiEOG092C37AK.

Enzyme and pathway databases

BioCyciYEAST:G3O-29631-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

EvolutionaryTraceiP49626.
PROiPR:P49626.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
InterProiView protein in InterPro
IPR025755. Ribos_L4_C_dom.
IPR002136. Ribosomal_L4/L1e.
IPR013000. Ribosomal_L4/L1e_euk/arc_CS.
IPR023574. Ribosomal_L4_dom.
PfamiView protein in Pfam
PF14374. Ribos_L4_asso_C. 1 hit.
PF00573. Ribosomal_L4. 1 hit.
SUPFAMiSSF52166. SSF52166. 1 hit.
PROSITEiView protein in PROSITE
PS00939. RIBOSOMAL_L1E. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRL4B_YEAST
AccessioniPrimary (citable) accession number: P49626
Secondary accession number(s): D6VRZ8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 23, 2007
Last modified: May 10, 2017
This is version 144 of the entry and version 2 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 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.