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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

Participates in the regulation of the accumulation of its own mRNA.

GO - Molecular functioni

  • RNA binding Source: UniProtKB-KW
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

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-B
Alternative name(s):
L2
RP2
YL2
Gene namesi
Name:RPL4B
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
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi95 – 951R → E: Leads to a slower growth at higher temperatures but allows RPL4 assembly into the 60S subunit; when associated with E-98. 1 Publication
Mutagenesisi98 – 981R → E: Leads to a slower growth at higher temperatures but allows RPL4 assembly into the mature 60S; when associated with E-95. 1 Publication
Mutagenesisi289 – 2891I → 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 Publication
Mutagenesisi290 – 2901I → 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 Publication
Mutagenesisi295 – 2951I → 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 Publication
Mutagenesisi314 – 3141K → A: Significantly diminished nuclear localization; when associated with A-315 and A-319. 1 Publication
Mutagenesisi315 – 3151K → A: Significantly diminished nuclear localization; when associated with A-314 and A-319. 1 Publication
Mutagenesisi319 – 3191K → A: Significantly diminished nuclear localization; when associated with A-314 and A-315. 1 Publication
Mutagenesisi332 – 3321K → E: Leads to an inefficient release from ACL4 with a delayed assembly into the 60S subunit; when associated with A-334. 1 Publication
Mutagenesisi334 – 3341F → A: Leads to an inefficient release from ACL4 with a delayed assembly into the 60S subunit; when associated with e-332. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 36236160S ribosomal protein L4-BPRO_0000129368Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine1 Publication

Post-translational modificationi

N-terminally acetylated by acetyltransferase NatA.1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP49626.
PeptideAtlasiP49626.
PRIDEiP49626.

PTM databases

iPTMnetiP49626.

Interactioni

Subunit structurei

Component of the large 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).Interacts with its chaperone ACL4 and the nuclear import receptor KAP104 (PubMed:25936803).2 Publications

Protein-protein interaction databases

BioGridi32063. 76 interactions.
DIPiDIP-5367N.
IntActiP49626. 209 interactions.
MINTiMINT-8285174.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2WW9electron microscopy8.60H1-362[»]
2WWAelectron microscopy8.90H1-362[»]
2WWBelectron microscopy6.48H1-362[»]
4V4Belectron microscopy11.70BD2-362[»]
ProteinModelPortaliP49626.
SMRiP49626. Positions 1-269.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP49626.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni277 – 36286C-terminal-extended nuclear localization signal1 PublicationAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the ribosomal protein L4P family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000018145.
HOGENOMiHOG000107331.
InParanoidiP49626.
KOiK02930.
OMAiINVAQKR.
OrthoDBiEOG7NSBC8.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
InterProiIPR025755. Ribos_L4_C_dom.
IPR002136. Ribosomal_L4/L1e.
IPR013000. Ribosomal_L4/L1e_euk/arc_CS.
IPR023574. Ribosomal_L4_dom.
[Graphical view]
PfamiPF14374. Ribos_L4_asso_C. 1 hit.
PF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMiSSF52166. SSF52166. 1 hit.
PROSITEiPS00939. RIBOSOMAL_L1E. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti88 – 881G → R in AAA34975 (PubMed:3062369).Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2WW9electron microscopy8.60H1-362[»]
2WWAelectron microscopy8.90H1-362[»]
2WWBelectron microscopy6.48H1-362[»]
4V4Belectron microscopy11.70BD2-362[»]
ProteinModelPortaliP49626.
SMRiP49626. Positions 1-269.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32063. 76 interactions.
DIPiDIP-5367N.
IntActiP49626. 209 interactions.
MINTiMINT-8285174.

PTM databases

iPTMnetiP49626.

Proteomic databases

MaxQBiP49626.
PeptideAtlasiP49626.
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.
OMAiINVAQKR.
OrthoDBiEOG7NSBC8.

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.
NextBioi969031.
PROiP49626.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
InterProiIPR025755. Ribos_L4_C_dom.
IPR002136. Ribosomal_L4/L1e.
IPR013000. Ribosomal_L4/L1e_euk/arc_CS.
IPR023574. Ribosomal_L4_dom.
[Graphical view]
PfamiPF14374. Ribos_L4_asso_C. 1 hit.
PF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMiSSF52166. SSF52166. 1 hit.
PROSITEiPS00939. RIBOSOMAL_L1E. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequencing and analysis of a 35.4 kb region on the right arm of chromosome IV from Saccharomyces cerevisiae reveal 23 open reading frames."
    Eide L.G., Sander C., Prydz H.
    Yeast 12:1085-1090(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. "Gene dosage alteration of L2 ribosomal protein genes in Saccharomyces cerevisiae: effects on ribosome synthesis."
    Lucioli A., Presutti C., Ciafre S., Caffarelli E., Fragapane P., Bozzoni I.
    Mol. Cell. Biol. 8:4792-4798(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-200.
  6. "NH2-terminal acetylation of ribosomal proteins of Saccharomyces cerevisiae."
    Takakura H., Tsunasawa S., Miyagi M., Warner J.R.
    J. Biol. Chem. 267:5442-5445(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-21, ACETYLATION AT SER-2 BY NATA.
  7. "The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae."
    Planta R.J., Mager W.H.
    Yeast 14:471-477(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE, SUBUNIT.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "Coordinated ribosomal L4 protein assembly into the pre-ribosome is regulated by its eukaryote-specific extension."
    Stelter P., Huber F.M., Kunze R., Flemming D., Hoelz A., Hurt E.
    Mol. Cell 58:854-862(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, INTERACTION WITH ACL4 AND KAP104, DOMAIN, SUBCELLULAR LOCATION, MUTAGENESIS OF ARG-95; ARG-98; ILE-289; ILE-290; ILE-295; LYS-314; LYS-315; LYS-319; LYS-332 AND PHE-334.
  11. "Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation."
    Spahn C.M.T., Gomez-Lorenzo M.G., Grassucci R.A., Joergensen R., Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P.G., Frank J.
    EMBO J. 23:1008-1019(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING, ELECTRON MICROSCOPY.

Entry informationi

Entry nameiRL4B_YEAST
AccessioniPrimary (citable) accession number: P49626
Secondary accession number(s): D6VRZ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 135 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 151000 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for L4 in yeast.

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.