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Protein

60S ribosomal protein L5

Gene

RPL5

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

Binds 5S RNA and is required for 60S subunit assembly.

GO - Molecular functioni

  1. 5S rRNA binding Source: SGD
  2. structural constituent of ribosome Source: SGD

GO - Biological processi

  1. cytoplasmic translation Source: SGD
  2. ribosomal large subunit assembly Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-34030-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.

Names & Taxonomyi

Protein namesi
Recommended name:
60S ribosomal protein L5
Alternative name(s):
L1
L1a
Ribosomal 5S RNA-binding protein
YL3
Gene namesi
Name:RPL5
Synonyms:RPL1, RPL1A
Ordered Locus Names:YPL131W
ORF Names:LPI14W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XVI

Organism-specific databases

SGDiS000006052. RPL5.

Subcellular locationi

Cytoplasm. Nucleus
Note: The SYO1/RPL11/RPL5 complex is transported into the nucleus by KAP104.

GO - Cellular componenti

  1. cytosolic large ribosomal subunit Source: SGD
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 29729660S ribosomal protein L5PRO_0000131454Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei167 – 1671Phosphoserine1 Publication
Modified residuei176 – 1761Phosphoserine1 Publication
Modified residuei235 – 2351Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP26321.
PaxDbiP26321.
PeptideAtlasiP26321.

Expressioni

Gene expression databases

GenevestigatoriP26321.

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). Forms a heterotrimeric complex with SYO1 and RPL11A or RPL11B. Interaction of this complex with KAP104 allows the nuclear import of the heterotrimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
NOG1Q028922EBI-15398,EBI-12105

Protein-protein interaction databases

BioGridi36050. 137 interactions.
DIPiDIP-1790N.
IntActiP26321. 163 interactions.
MINTiMINT-8285488.
STRINGi4932.YPL131W.

Structurei

Secondary structure

1
297
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 74Combined sources
Helixi10 – 145Combined sources
Helixi21 – 244Combined sources
Helixi30 – 378Combined sources
Helixi41 – 433Combined sources
Beta strandi50 – 567Combined sources
Beta strandi59 – 6810Combined sources
Beta strandi71 – 799Combined sources
Helixi80 – 867Combined sources
Beta strandi92 – 943Combined sources
Helixi95 – 11218Combined sources
Beta strandi116 – 1183Combined sources
Beta strandi136 – 1383Combined sources
Beta strandi145 – 1473Combined sources
Helixi159 – 16810Combined sources
Helixi177 – 1793Combined sources
Beta strandi180 – 1845Combined sources
Turni185 – 1884Combined sources
Helixi192 – 1998Combined sources
Helixi202 – 21413Combined sources
Helixi216 – 2216Combined sources
Helixi224 – 2285Combined sources
Helixi233 – 2353Combined sources
Helixi236 – 24914Combined sources
Helixi262 – 2709Combined sources
Beta strandi271 – 2733Combined sources
Helixi279 – 29214Combined sources
Turni293 – 2964Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-E11-232[»]
3J6Xelectron microscopy6.10L51-297[»]
3J6Yelectron microscopy6.10L51-297[»]
3J77electron microscopy6.20L51-297[»]
3J78electron microscopy6.30L51-297[»]
4U3MX-ray3.00L5/l52-297[»]
4U3NX-ray3.20L5/l52-297[»]
4U3UX-ray2.90L5/l52-297[»]
4U4NX-ray3.10L5/l52-297[»]
4U4OX-ray3.60L5/l52-297[»]
4U4QX-ray3.00L5/l52-297[»]
4U4RX-ray2.80L5/l52-297[»]
4U4UX-ray3.00L5/l52-297[»]
4U4YX-ray3.20L5/l52-297[»]
4U4ZX-ray3.10L5/l52-297[»]
4U50X-ray3.20L5/l52-297[»]
4U51X-ray3.20L5/l52-297[»]
4U52X-ray3.00L5/l52-297[»]
4U53X-ray3.30L5/l52-297[»]
4U55X-ray3.20L5/l52-297[»]
4U56X-ray3.45L5/l52-297[»]
4U6FX-ray3.10L5/l52-297[»]
4V4Belectron microscopy11.70BE11-232[»]
4V6Ielectron microscopy8.80BQ1-297[»]
4V7Felectron microscopy8.70P1-297[»]
4V7RX-ray4.00BE/DE1-297[»]
4V88X-ray3.00BD/DD1-297[»]
4V8Telectron microscopy8.10D1-297[»]
4V8Yelectron microscopy4.30BD2-297[»]
4V8Zelectron microscopy6.60BD2-297[»]
4V91electron microscopy3.70D1-297[»]
ProteinModelPortaliP26321.
SMRiP26321. Positions 2-297.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP26321.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L18P family.Curated

Phylogenomic databases

eggNOGiCOG0256.
GeneTreeiENSGT00390000008456.
HOGENOMiHOG000105947.
InParanoidiP26321.
KOiK02932.
OMAiEDPFKKV.
OrthoDBiEOG7DJSXQ.

Family and domain databases

HAMAPiMF_01337_A. Ribosomal_L18_A.
InterProiIPR005485. Rbsml_L5_euk/L18_arc.
IPR025607. Rbsml_L5e/L18P_C.
IPR005484. Ribosomal_L18/L5.
[Graphical view]
PANTHERiPTHR23410. PTHR23410. 1 hit.
PfamiPF14204. Ribosomal_L18_c. 1 hit.
PF00861. Ribosomal_L18p. 1 hit.
[Graphical view]
PRINTSiPR00058. RIBOSOMALL5.

Sequencei

Sequence statusi: Complete.

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

P26321-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAFQKDAKSS AYSSRFQTPF RRRREGKTDY YQRKRLVTQH KAKYNTPKYR
60 70 80 90 100
LVVRFTNKDI ICQIISSTIT GDVVLAAAYS HELPRYGITH GLTNWAAAYA
110 120 130 140 150
TGLLIARRTL QKLGLDETYK GVEEVEGEYE LTEAVEDGPR PFKVFLDIGL
160 170 180 190 200
QRTTTGARVF GALKGASDGG LYVPHSENRF PGWDFETEEI DPELLRSYIF
210 220 230 240 250
GGHVSQYMEE LADDDEERFS ELFKGYLADD IDADSLEDIY TSAHEAIRAD
260 270 280 290
PAFKPTEKKF TKEQYAAESK KYRQTKLSKE ERAARVAAKI AALAGQQ
Length:297
Mass (Da):33,715
Last modified:October 4, 2010 - v4
Checksum:i14E3B2931C3CAE2B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti18 – 181T → Y AA sequence (PubMed:393511).Curated
Sequence conflicti112 – 1121K → R in AAA35234 (PubMed:2007570).Curated
Sequence conflicti112 – 1121K → R in AAA35236 (PubMed:1325447).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M65056 Genomic DNA. Translation: AAA35234.1.
M94864 Genomic DNA. Translation: AAA35236.1.
L01796 Genomic DNA. Translation: AAA34979.1.
U43703 Genomic DNA. Translation: AAB68228.1.
BK006949 Genomic DNA. Translation: DAA11302.1.
PIRiS42144.
RefSeqiNP_015194.1. NM_001183945.1.

Genome annotation databases

EnsemblFungiiYPL131W; YPL131W; YPL131W.
GeneIDi855972.
KEGGisce:YPL131W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M65056 Genomic DNA. Translation: AAA35234.1.
M94864 Genomic DNA. Translation: AAA35236.1.
L01796 Genomic DNA. Translation: AAA34979.1.
U43703 Genomic DNA. Translation: AAB68228.1.
BK006949 Genomic DNA. Translation: DAA11302.1.
PIRiS42144.
RefSeqiNP_015194.1. NM_001183945.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-E11-232[»]
3J6Xelectron microscopy6.10L51-297[»]
3J6Yelectron microscopy6.10L51-297[»]
3J77electron microscopy6.20L51-297[»]
3J78electron microscopy6.30L51-297[»]
4U3MX-ray3.00L5/l52-297[»]
4U3NX-ray3.20L5/l52-297[»]
4U3UX-ray2.90L5/l52-297[»]
4U4NX-ray3.10L5/l52-297[»]
4U4OX-ray3.60L5/l52-297[»]
4U4QX-ray3.00L5/l52-297[»]
4U4RX-ray2.80L5/l52-297[»]
4U4UX-ray3.00L5/l52-297[»]
4U4YX-ray3.20L5/l52-297[»]
4U4ZX-ray3.10L5/l52-297[»]
4U50X-ray3.20L5/l52-297[»]
4U51X-ray3.20L5/l52-297[»]
4U52X-ray3.00L5/l52-297[»]
4U53X-ray3.30L5/l52-297[»]
4U55X-ray3.20L5/l52-297[»]
4U56X-ray3.45L5/l52-297[»]
4U6FX-ray3.10L5/l52-297[»]
4V4Belectron microscopy11.70BE11-232[»]
4V6Ielectron microscopy8.80BQ1-297[»]
4V7Felectron microscopy8.70P1-297[»]
4V7RX-ray4.00BE/DE1-297[»]
4V88X-ray3.00BD/DD1-297[»]
4V8Telectron microscopy8.10D1-297[»]
4V8Yelectron microscopy4.30BD2-297[»]
4V8Zelectron microscopy6.60BD2-297[»]
4V91electron microscopy3.70D1-297[»]
ProteinModelPortaliP26321.
SMRiP26321. Positions 2-297.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36050. 137 interactions.
DIPiDIP-1790N.
IntActiP26321. 163 interactions.
MINTiMINT-8285488.
STRINGi4932.YPL131W.

Proteomic databases

MaxQBiP26321.
PaxDbiP26321.
PeptideAtlasiP26321.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL131W; YPL131W; YPL131W.
GeneIDi855972.
KEGGisce:YPL131W.

Organism-specific databases

SGDiS000006052. RPL5.

Phylogenomic databases

eggNOGiCOG0256.
GeneTreeiENSGT00390000008456.
HOGENOMiHOG000105947.
InParanoidiP26321.
KOiK02932.
OMAiEDPFKKV.
OrthoDBiEOG7DJSXQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-34030-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.

Miscellaneous databases

EvolutionaryTraceiP26321.
NextBioi980789.
PROiP26321.

Gene expression databases

GenevestigatoriP26321.

Family and domain databases

HAMAPiMF_01337_A. Ribosomal_L18_A.
InterProiIPR005485. Rbsml_L5_euk/L18_arc.
IPR025607. Rbsml_L5e/L18P_C.
IPR005484. Ribosomal_L18/L5.
[Graphical view]
PANTHERiPTHR23410. PTHR23410. 1 hit.
PfamiPF14204. Ribosomal_L18_c. 1 hit.
PF00861. Ribosomal_L18p. 1 hit.
[Graphical view]
PRINTSiPR00058. RIBOSOMALL5.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure of the yeast ribosomal 5 S RNA-binding protein YL3."
    Tang B., Nazar R.N.
    J. Biol. Chem. 266:6120-6123(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Unbalanced regulation of the ribosomal 5 S RNA-binding protein in Saccharomyces cerevisiae expressing mutant 5 S rRNAs."
    Tang B., Nazar R.N.
    J. Biol. Chem. 267:17738-17742(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits."
    Deshmukh M.P., Tsay Y.F., Paulovich A.G., Woolford J.L. Jr.
    Mol. Cell. Biol. 13:2835-2845(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "The 5-S RNA binding protein from yeast (Saccharomyces cerevisiae) ribosomes. Evolution of the eukaryotic 5-S RNA binding protein."
    Nazar R.N., Yaguchi M., Willick G.E., Rollin C.F., Roy C.
    Eur. J. Biochem. 102:573-582(1978) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-31 AND 219-253.
  7. "The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae."
    Planta R.J., Mager W.H.
    Yeast 14:471-477(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE, SUBUNIT.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-235, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  10. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-167; SER-176 AND SER-235, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
    Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
    Proteomics 12:236-240(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. Cited for: INTERACTION WITH RPL11A; RPL11B AND SYO1, SUBCELLULAR LOCATION.
  15. "Structure of the 80S ribosome from Saccharomyces cerevisiae -- tRNA-ribosome and subunit-subunit interactions."
    Spahn C.M.T., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J.
    Cell 107:373-386(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF 11-232, ELECTRON MICROSCOPY.
  16. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF 11-232, ELECTRON MICROSCOPY.
  17. "Crystal structure of the eukaryotic ribosome."
    Ben-Shem A., Jenner L., Yusupova G., Yusupov M.
    Science 330:1203-1209(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 80S RIBOSOME.
  18. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 80S RIBOSOME.

Entry informationi

Entry nameiRL5_YEAST
AccessioniPrimary (citable) accession number: P26321
Secondary accession number(s): D6W3N6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 30, 1992
Last sequence update: October 4, 2010
Last modified: March 31, 2015
This is version 141 of the entry and version 4 of the sequence. [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 XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

External Data

Dasty 3

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 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.