Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Exosome complex component CSL4

Gene

CSL4

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

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes.3 Publications

GO - Molecular functioni

GO - Biological processi

  • exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • ncRNA 3'-end processing Source: SGD
  • nonfunctional rRNA decay Source: SGD
  • nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  • nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  • nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  • polyadenylation-dependent snoRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33232-MONOMER.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component CSL4
Alternative name(s):
CEP1 synthetic lethal protein 4
Gene namesi
Name:CSL4
Synonyms:SKI4
Ordered Locus Names:YNL232W
ORF Names:N1154
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL232W.
SGDiS000005176. CSL4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic exosome (RNase complex) Source: SGD
  • nuclear exosome (RNase complex) Source: SGD
  • nucleolus Source: UniProtKB-SubCell
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000794031 – 292Exosome complex component CSL4Add BLAST292

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei94PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53859.
PRIDEiP53859.

PTM databases

iPTMnetiP53859.

Interactioni

Subunit structurei

Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits and peripheral S1 domain-containing components CSL4, RRP4 and RRP40 located on the top of the ring structure.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
MTR3P482408EBI-1731,EBI-1749
RRP4P387927EBI-1731,EBI-1757
RRP40Q082855EBI-1731,EBI-1831
RRP42Q122778EBI-1731,EBI-1765
RRP43P253597EBI-1731,EBI-1773
RRP45Q056367EBI-1731,EBI-1810
RRP46P532567EBI-1731,EBI-1842
SKI6P469489EBI-1731,EBI-1788
SKI7Q084915EBI-1731,EBI-1389

Protein-protein interaction databases

BioGridi35606. 48 interactors.
DIPiDIP-6785N.
IntActiP53859. 17 interactors.
MINTiMINT-614245.

Structurei

Secondary structure

1292
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi9 – 11Combined sources3
Beta strandi15 – 23Combined sources9
Beta strandi32 – 37Combined sources6
Beta strandi41 – 48Combined sources8
Beta strandi51 – 58Combined sources8
Beta strandi60 – 67Combined sources8
Beta strandi106 – 112Combined sources7
Beta strandi138 – 146Combined sources9
Beta strandi148 – 160Combined sources13
Beta strandi162 – 165Combined sources4
Helixi183 – 186Combined sources4
Turni190 – 192Combined sources3
Turni195 – 198Combined sources4
Beta strandi202 – 206Combined sources5
Helixi207 – 209Combined sources3
Beta strandi212 – 214Combined sources3
Helixi215 – 217Combined sources3
Helixi220 – 222Combined sources3
Beta strandi229 – 236Combined sources8
Beta strandi240 – 246Combined sources7
Beta strandi253 – 256Combined sources4
Turni259 – 263Combined sources5
Beta strandi268 – 271Combined sources4
Beta strandi274 – 276Combined sources3
Turni278 – 280Combined sources3
Beta strandi283 – 285Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80I1-292[»]
4OO1X-ray3.30I1-292[»]
5C0WX-ray4.60I1-292[»]
5C0XX-ray3.81I1-292[»]
5G06electron microscopy4.20I1-292[»]
5JEAX-ray2.65I1-292[»]
ProteinModelPortaliP53859.
SMRiP53859.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the CSL4 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000015287.
HOGENOMiHOG000177330.
InParanoidiP53859.
KOiK07573.
OMAiMYAIDWQ.
OrthoDBiEOG092C53BP.

Family and domain databases

InterProiIPR019495. EXOSC1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF10447. EXOSC1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 2 hits.

Sequencei

Sequence statusi: Complete.

P53859-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MACNFQFPEI AYPGKLICPQ YGTENKDGED IIFNYVPGPG TKLIQYEHNG
60 70 80 90 100
RTLEAITATL VGTVRCEEEK KTDQEEEREG TDQSTEEEKS VDASPNDVTR
110 120 130 140 150
RTVKNILVSV LPGTEKGRKT NKYANNDFAN NLPKEGDIVL TRVTRLSLQR
160 170 180 190 200
ANVEILAVED KPSPIDSGIG SNGSGIVAAG GGSGAATFSV SQASSDLGET
210 220 230 240 250
FRGIIRSQDV RSTDRDRVKV IECFKPGDIV RAQVLSLGDG TNYYLTTARN
260 270 280 290
DLGVVFARAA NGAGGLMYAT DWQMMTSPVT GATEKRKCAK PF
Length:292
Mass (Da):31,583
Last modified:October 1, 1996 - v1
Checksum:i52D3416EA183583B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z69381 Genomic DNA. Translation: CAA93366.1.
Z71508 Genomic DNA. Translation: CAA96137.1.
BK006947 Genomic DNA. Translation: DAA10326.1.
PIRiS63198.
RefSeqiNP_014167.1. NM_001183070.1.

Genome annotation databases

EnsemblFungiiYNL232W; YNL232W; YNL232W.
GeneIDi855489.
KEGGisce:YNL232W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z69381 Genomic DNA. Translation: CAA93366.1.
Z71508 Genomic DNA. Translation: CAA96137.1.
BK006947 Genomic DNA. Translation: DAA10326.1.
PIRiS63198.
RefSeqiNP_014167.1. NM_001183070.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80I1-292[»]
4OO1X-ray3.30I1-292[»]
5C0WX-ray4.60I1-292[»]
5C0XX-ray3.81I1-292[»]
5G06electron microscopy4.20I1-292[»]
5JEAX-ray2.65I1-292[»]
ProteinModelPortaliP53859.
SMRiP53859.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35606. 48 interactors.
DIPiDIP-6785N.
IntActiP53859. 17 interactors.
MINTiMINT-614245.

PTM databases

iPTMnetiP53859.

Proteomic databases

MaxQBiP53859.
PRIDEiP53859.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL232W; YNL232W; YNL232W.
GeneIDi855489.
KEGGisce:YNL232W.

Organism-specific databases

EuPathDBiFungiDB:YNL232W.
SGDiS000005176. CSL4.

Phylogenomic databases

GeneTreeiENSGT00390000015287.
HOGENOMiHOG000177330.
InParanoidiP53859.
KOiK07573.
OMAiMYAIDWQ.
OrthoDBiEOG092C53BP.

Enzyme and pathway databases

BioCyciYEAST:G3O-33232-MONOMER.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

PROiP53859.

Family and domain databases

InterProiIPR019495. EXOSC1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF10447. EXOSC1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 2 hits.
ProtoNetiSearch...

Entry informationi

Entry nameiCSL4_YEAST
AccessioniPrimary (citable) accession number: P53859
Secondary accession number(s): D6W0W0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 146 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 5550 molecules/cell in log phase SD medium.1 Publication

Caution

According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: 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.