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Protein

60S ribosomal protein L13-A

Gene

RPL13A

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-29491-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-A
Gene namesi
Name:RPL13A
Ordered Locus Names:YDL082W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL082W.
SGDiS000002240. RPL13A.

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
Chaini1 – 19919960S ribosomal protein L13-APRO_0000192938Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei144 – 1441PhosphothreonineBy similarity
Modified residuei152 – 1521PhosphothreonineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ12690.
PeptideAtlasiQ12690.
TopDownProteomicsiQ12690.

PTM databases

iPTMnetiQ12690.

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

BioGridi31979. 104 interactions.
IntActiQ12690. 23 interactions.
MINTiMINT-2981666.

Structurei

Secondary structure

1
199
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi18 – 203Combined sources
Beta strandi21 – 244Combined sources
Helixi25 – 273Combined sources
Helixi28 – 4518Combined sources
Turni46 – 483Combined sources
Beta strandi57 – 593Combined sources
Helixi62 – 654Combined sources
Beta strandi68 – 714Combined sources
Helixi77 – 826Combined sources
Helixi87 – 926Combined sources
Helixi106 – 12116Combined sources
Beta strandi123 – 1253Combined sources
Beta strandi128 – 1303Combined sources
Turni142 – 1443Combined sources
Beta strandi155 – 1573Combined sources
Helixi166 – 17813Combined sources
Helixi180 – 19112Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10531-199[»]
3J6Yelectron microscopy6.10531-199[»]
3J77electron microscopy6.20631-199[»]
3J78electron microscopy6.30631-199[»]
4U3MX-ray3.00M3/m32-199[»]
4U3NX-ray3.20M3/m32-199[»]
4U3UX-ray2.90M3/m32-199[»]
4U4NX-ray3.10M3/m32-199[»]
4U4OX-ray3.60M3/m32-199[»]
4U4QX-ray3.00M3/m32-199[»]
4U4RX-ray2.80M3/m32-199[»]
4U4UX-ray3.00M3/m32-199[»]
4U4YX-ray3.20M3/m32-199[»]
4U4ZX-ray3.10M3/m32-199[»]
4U50X-ray3.20M3/m32-199[»]
4U51X-ray3.20M3/m32-199[»]
4U52X-ray3.00M3/m32-199[»]
4U53X-ray3.30M3/m32-199[»]
4U55X-ray3.20M3/m32-199[»]
4U56X-ray3.45M3/m32-199[»]
4U6FX-ray3.10M3/m32-199[»]
4V7Felectron microscopy8.70K1-199[»]
4V88X-ray3.00BL/DL1-199[»]
4V8Telectron microscopy8.10L1-199[»]
4V8Yelectron microscopy4.30BL2-199[»]
4V8Zelectron microscopy6.60BL2-199[»]
5APNelectron microscopy3.91L1-199[»]
5APOelectron microscopy3.41L1-199[»]
5FL8electron microscopy9.50L1-199[»]
5GAKelectron microscopy3.88N1-199[»]
ProteinModelPortaliQ12690.
SMRiQ12690. Positions 2-195.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L13e family.Curated

Phylogenomic databases

HOGENOMiHOG000170452.
InParanoidiQ12690.
KOiK02873.
OMAiISNHFRK.
OrthoDBiEOG7W9S6G.

Family and domain databases

InterProiIPR001380. Ribosomal_L13e.
IPR018256. Ribosomal_L13e_CS.
[Graphical view]
PANTHERiPTHR11722. PTHR11722. 1 hit.
PfamiPF01294. Ribosomal_L13e. 1 hit.
[Graphical view]
PROSITEiPS01104. RIBOSOMAL_L13E. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q12690-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAISKNLPIL KNHFRKHWQE RVKVHFDQAG KKVSRRNARA TRAAKIAPRP
60 70 80 90 100
LDLLRPVVRA PTVKYNRKVR AGRGFTLAEV KAAGLTAAYA RTIGIAVDHR
110 120 130 140 150
RQNRNQEIFD ANVQRLKEYQ SKIIVFPRNG KAPEAEQVLS AAATFPIAQP
160 170 180 190
ATDVEARAVQ DNGESAFRTL RLARSEKKFR GIREKRAREK AEAEAEKKK
Length:199
Mass (Da):22,554
Last modified:November 1, 1996 - v1
Checksum:iEA7CC5F1F3C0335A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74130 Genomic DNA. Translation: CAA98648.1.
BK006938 Genomic DNA. Translation: DAA11777.1.
PIRiS67618.
RefSeqiNP_010201.1. NM_001180141.1.

Genome annotation databases

EnsemblFungiiYDL082W; YDL082W; YDL082W.
GeneIDi851477.
KEGGisce:YDL082W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74130 Genomic DNA. Translation: CAA98648.1.
BK006938 Genomic DNA. Translation: DAA11777.1.
PIRiS67618.
RefSeqiNP_010201.1. NM_001180141.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10531-199[»]
3J6Yelectron microscopy6.10531-199[»]
3J77electron microscopy6.20631-199[»]
3J78electron microscopy6.30631-199[»]
4U3MX-ray3.00M3/m32-199[»]
4U3NX-ray3.20M3/m32-199[»]
4U3UX-ray2.90M3/m32-199[»]
4U4NX-ray3.10M3/m32-199[»]
4U4OX-ray3.60M3/m32-199[»]
4U4QX-ray3.00M3/m32-199[»]
4U4RX-ray2.80M3/m32-199[»]
4U4UX-ray3.00M3/m32-199[»]
4U4YX-ray3.20M3/m32-199[»]
4U4ZX-ray3.10M3/m32-199[»]
4U50X-ray3.20M3/m32-199[»]
4U51X-ray3.20M3/m32-199[»]
4U52X-ray3.00M3/m32-199[»]
4U53X-ray3.30M3/m32-199[»]
4U55X-ray3.20M3/m32-199[»]
4U56X-ray3.45M3/m32-199[»]
4U6FX-ray3.10M3/m32-199[»]
4V7Felectron microscopy8.70K1-199[»]
4V88X-ray3.00BL/DL1-199[»]
4V8Telectron microscopy8.10L1-199[»]
4V8Yelectron microscopy4.30BL2-199[»]
4V8Zelectron microscopy6.60BL2-199[»]
5APNelectron microscopy3.91L1-199[»]
5APOelectron microscopy3.41L1-199[»]
5FL8electron microscopy9.50L1-199[»]
5GAKelectron microscopy3.88N1-199[»]
ProteinModelPortaliQ12690.
SMRiQ12690. Positions 2-195.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31979. 104 interactions.
IntActiQ12690. 23 interactions.
MINTiMINT-2981666.

PTM databases

iPTMnetiQ12690.

Proteomic databases

MaxQBiQ12690.
PeptideAtlasiQ12690.
TopDownProteomicsiQ12690.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL082W; YDL082W; YDL082W.
GeneIDi851477.
KEGGisce:YDL082W.

Organism-specific databases

EuPathDBiFungiDB:YDL082W.
SGDiS000002240. RPL13A.

Phylogenomic databases

HOGENOMiHOG000170452.
InParanoidiQ12690.
KOiK02873.
OMAiISNHFRK.
OrthoDBiEOG7W9S6G.

Enzyme and pathway databases

BioCyciYEAST:G3O-29491-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

NextBioi968783.
PROiQ12690.

Family and domain databases

InterProiIPR001380. Ribosomal_L13e.
IPR018256. Ribosomal_L13e_CS.
[Graphical view]
PANTHERiPTHR11722. PTHR11722. 1 hit.
PfamiPF01294. Ribosomal_L13e. 1 hit.
[Graphical view]
PROSITEiPS01104. RIBOSOMAL_L13E. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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.
  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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "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.
  7. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 80S RIBOSOME.

Entry informationi

Entry nameiRL13A_YEAST
AccessioniPrimary (citable) accession number: Q12690
Secondary accession number(s): D6VRR7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: May 11, 2016
This is version 128 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 133000 molecules/cell in log phase SD medium.1 Publication
There are 2 genes for L13 in yeast.

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 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.