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Protein

60S ribosomal protein L38

Gene

RPL38

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

  • structural constituent of ribosome Source: SGD

GO - Biological processi

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

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-32408-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 L38
Gene namesi
Name:RPL38
Ordered Locus Names:YLR325C
ORF Names:L8543.2
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XII

Organism-specific databases

CYGDiYLR325c.
EuPathDBiFungiDB:YLR325C.
SGDiS000004317. RPL38.

Subcellular locationi

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 787760S ribosomal protein L38PRO_0000215445Add
BLAST

Proteomic databases

MaxQBiP49167.
PaxDbiP49167.
PeptideAtlasiP49167.

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).1 Publication

Protein-protein interaction databases

BioGridi31588. 46 interactions.
DIPiDIP-3950N.
IntActiP49167. 12 interactions.
MINTiMINT-8285362.

Structurei

Secondary structure

1
78
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 53Combined sources
Helixi8 – 147Combined sources
Beta strandi17 – 193Combined sources
Beta strandi22 – 3110Combined sources
Beta strandi33 – 353Combined sources
Beta strandi37 – 4610Combined sources
Beta strandi51 – 566Combined sources
Helixi59 – 6810Combined sources
Beta strandi73 – 775Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10781-78[»]
3J6Yelectron microscopy6.10781-78[»]
3J77electron microscopy6.20881-78[»]
3J78electron microscopy6.30881-78[»]
4U3MX-ray3.00O8/o82-78[»]
4U3NX-ray3.20O8/o82-78[»]
4U3UX-ray2.90O8/o82-78[»]
4U4NX-ray3.10O8/o82-78[»]
4U4OX-ray3.60O8/o82-78[»]
4U4QX-ray3.00O8/o82-78[»]
4U4RX-ray2.80O8/o82-78[»]
4U4UX-ray3.00O8/o82-78[»]
4U4YX-ray3.20O8/o82-78[»]
4U4ZX-ray3.10O8/o82-78[»]
4U50X-ray3.20O8/o82-78[»]
4U51X-ray3.20O8/o82-78[»]
4U52X-ray3.00O8/o82-78[»]
4U53X-ray3.30O8/o82-78[»]
4U55X-ray3.20O8/o82-78[»]
4U56X-ray3.45O8/o82-78[»]
4U6FX-ray3.10O8/o82-78[»]
4V6Ielectron microscopy8.80Bn1-78[»]
4V7Felectron microscopy8.70i1-78[»]
4V88X-ray3.00Bk/Dk1-78[»]
4V8Telectron microscopy8.10k1-78[»]
4V8Yelectron microscopy4.30Bk2-78[»]
4V8Zelectron microscopy6.60Bk2-78[»]
4V91electron microscopy3.70k1-78[»]
ProteinModelPortaliP49167.
SMRiP49167. Positions 2-78.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L38e family.Curated

Phylogenomic databases

eggNOGiNOG323549.
GeneTreeiENSGT00390000003718.
HOGENOMiHOG000188979.
InParanoidiP49167.
KOiK02923.
OMAiQYTLVVN.
OrthoDBiEOG7FFN53.

Family and domain databases

InterProiIPR002675. Ribosomal_L38e.
[Graphical view]
PANTHERiPTHR10965. PTHR10965. 1 hit.
PfamiPF01781. Ribosomal_L38e. 1 hit.
[Graphical view]
ProDomiPD010361. Ribosomal_L38e. 1 hit.
[Graphical view] [Entries sharing at least one domain]

Sequencei

Sequence statusi: Complete.

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

P49167-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAREITDIKQ FLELTRRADV KTATVKINKK LNKAGKPFRQ TKFKVRGSSS
60 70
LYTLVINDAG KAKKLIQSLP PTLKVNRL
Length:78
Mass (Da):8,827
Last modified:February 1, 1996 - v1
Checksum:i0ECB20AD9A4A0D42
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20618 Genomic DNA. Translation: AAB64512.1.
BK006945 Genomic DNA. Translation: DAA09633.1.
PIRiS53402.
RefSeqiNP_013429.1. NM_001182214.1.

Genome annotation databases

EnsemblFungiiYLR325C; YLR325C; YLR325C.
GeneIDi851035.
KEGGisce:YLR325C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20618 Genomic DNA. Translation: AAB64512.1.
BK006945 Genomic DNA. Translation: DAA09633.1.
PIRiS53402.
RefSeqiNP_013429.1. NM_001182214.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10781-78[»]
3J6Yelectron microscopy6.10781-78[»]
3J77electron microscopy6.20881-78[»]
3J78electron microscopy6.30881-78[»]
4U3MX-ray3.00O8/o82-78[»]
4U3NX-ray3.20O8/o82-78[»]
4U3UX-ray2.90O8/o82-78[»]
4U4NX-ray3.10O8/o82-78[»]
4U4OX-ray3.60O8/o82-78[»]
4U4QX-ray3.00O8/o82-78[»]
4U4RX-ray2.80O8/o82-78[»]
4U4UX-ray3.00O8/o82-78[»]
4U4YX-ray3.20O8/o82-78[»]
4U4ZX-ray3.10O8/o82-78[»]
4U50X-ray3.20O8/o82-78[»]
4U51X-ray3.20O8/o82-78[»]
4U52X-ray3.00O8/o82-78[»]
4U53X-ray3.30O8/o82-78[»]
4U55X-ray3.20O8/o82-78[»]
4U56X-ray3.45O8/o82-78[»]
4U6FX-ray3.10O8/o82-78[»]
4V6Ielectron microscopy8.80Bn1-78[»]
4V7Felectron microscopy8.70i1-78[»]
4V88X-ray3.00Bk/Dk1-78[»]
4V8Telectron microscopy8.10k1-78[»]
4V8Yelectron microscopy4.30Bk2-78[»]
4V8Zelectron microscopy6.60Bk2-78[»]
4V91electron microscopy3.70k1-78[»]
ProteinModelPortaliP49167.
SMRiP49167. Positions 2-78.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31588. 46 interactions.
DIPiDIP-3950N.
IntActiP49167. 12 interactions.
MINTiMINT-8285362.

Proteomic databases

MaxQBiP49167.
PaxDbiP49167.
PeptideAtlasiP49167.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR325C; YLR325C; YLR325C.
GeneIDi851035.
KEGGisce:YLR325C.

Organism-specific databases

CYGDiYLR325c.
EuPathDBiFungiDB:YLR325C.
SGDiS000004317. RPL38.

Phylogenomic databases

eggNOGiNOG323549.
GeneTreeiENSGT00390000003718.
HOGENOMiHOG000188979.
InParanoidiP49167.
KOiK02923.
OMAiQYTLVVN.
OrthoDBiEOG7FFN53.

Enzyme and pathway databases

BioCyciYEAST:G3O-32408-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

NextBioi967628.
PROiP49167.

Family and domain databases

InterProiIPR002675. Ribosomal_L38e.
[Graphical view]
PANTHERiPTHR10965. PTHR10965. 1 hit.
PfamiPF01781. Ribosomal_L38e. 1 hit.
[Graphical view]
ProDomiPD010361. Ribosomal_L38e. 1 hit.
[Graphical view] [Entries sharing at least one domain]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "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.
  4. "The action of N-terminal acetyltransferases on yeast ribosomal proteins."
    Arnold R.J., Polevoda B., Reilly J.P., Sherman F.
    J. Biol. Chem. 274:37035-37040(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CLEAVAGE OF INITIATOR METHIONINE.
  5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
    Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
    Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: YAL6B.
  8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "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(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "Crystal structure of the eukaryotic ribosome."
    Ben-Shem A., Jenner L., Yusupova G., Yusupov M.
    Science 330:1203-1209(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 80S RIBOSOME.
  11. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 80S RIBOSOME.

Entry informationi

Entry nameiRL38_YEAST
AccessioniPrimary (citable) accession number: P49167
Secondary accession number(s): D6VYW7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: July 22, 2015
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 50200 molecules/cell in log phase SD medium.1 Publication

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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.