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Protein

Exosome complex component Csl4

Gene

csl4

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Increases the RNA binding and the efficiency of RNA degradation. Helpful for the interaction of the exosome with A-poor RNAs (Probable).2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi143 – 1431ZincUniRule annotation2 Publications
Metal bindingi146 – 1461ZincUniRule annotation2 Publications
Metal bindingi159 – 1591ZincUniRule annotation2 Publications
Metal bindingi162 – 1621ZincUniRule annotation2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-210-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Csl4UniRule annotation
Gene namesi
Name:csl4UniRule annotation
Ordered Locus Names:AF_0206
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 179179Exosome complex component Csl4PRO_0000424720Add
BLAST

Interactioni

Subunit structurei

Component of the archaeal exosome complex. Forms a trimer of Rrp4 and/or Csl4 subunits. The trimer associates with a hexameric ring-like arrangement composed of 3 Rrp41-Rrp42 heterodimers. Interacts with DnaG (Probable).2 Publications

Protein-protein interaction databases

STRINGi224325.AF0206.

Structurei

Secondary structure

1
179
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 124Combined sources
Turni13 – 153Combined sources
Beta strandi16 – 183Combined sources
Beta strandi22 – 254Combined sources
Beta strandi28 – 4013Combined sources
Beta strandi43 – 508Combined sources
Beta strandi60 – 689Combined sources
Beta strandi70 – 8011Combined sources
Beta strandi91 – 966Combined sources
Helixi97 – 993Combined sources
Helixi108 – 1103Combined sources
Beta strandi117 – 1248Combined sources
Turni125 – 1273Combined sources
Beta strandi128 – 1303Combined sources
Beta strandi133 – 1353Combined sources
Beta strandi137 – 1404Combined sources
Turni144 – 1463Combined sources
Beta strandi151 – 1533Combined sources
Beta strandi154 – 1585Combined sources
Beta strandi160 – 1623Combined sources
Turni172 – 1776Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BA1X-ray2.70A/B/C1-179[»]
3M7NX-ray2.40A/B/C1-179[»]
3M85X-ray3.00A/B/C1-179[»]
ProteinModelPortaliO30033.
SMRiO30033. Positions 1-179.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO30033.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini58 – 13780S1 motifUniRule annotationAdd
BLAST

Domaini

Contains an N-terminal domain that mediates interactions with the hexameric ring, a central S1 domain and a C-terminal zinc-ribbon domain.1 Publication

Sequence similaritiesi

Belongs to the CSL4 family.UniRule annotation
Contains 1 S1 motif domain.UniRule annotation

Phylogenomic databases

eggNOGiarCOG00676. Archaea.
COG1096. LUCA.
KOiK07573.
OMAiCGNVETR.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_00975. Exosome_Csl4.
InterProiIPR019495. EXOSC1.
IPR025721. Exosome_cplx_N_dom.
IPR030850. Exosome_Csl4_arc.
IPR012340. NA-bd_OB-fold.
IPR022967. S1_dom.
[Graphical view]
PfamiPF14382. ECR1_N. 1 hit.
PF10447. EXOSC1. 1 hit.
[Graphical view]
SMARTiSM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.

Sequencei

Sequence statusi: Complete.

O30033-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRFVMPGDRI GSAEEYVKGE GVYEEGGELF AAVAGKLIIK DRVAKVESIS
60 70 80 90 100
PIPEIVKGDV VLGRVVDLRN SIALIEVSSK KGENRGPSNR GIGILHVSNV
110 120 130 140 150
DEGYVKEISE AVGYLDILKA RVIGDNLRLS TKEEEMGVLR ALCSNCKTEM
160 170
VREGDILKCP ECGRVEKRKI STDYGKGEW
Length:179
Mass (Da):19,597
Last modified:January 1, 1998 - v1
Checksum:i3106D5592EF6EAF7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB91036.1.
PIRiF69275.
RefSeqiWP_010877717.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB91036; AAB91036; AF_0206.
GeneIDi24793740.
KEGGiafu:AF_0206.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB91036.1.
PIRiF69275.
RefSeqiWP_010877717.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BA1X-ray2.70A/B/C1-179[»]
3M7NX-ray2.40A/B/C1-179[»]
3M85X-ray3.00A/B/C1-179[»]
ProteinModelPortaliO30033.
SMRiO30033. Positions 1-179.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0206.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB91036; AAB91036; AF_0206.
GeneIDi24793740.
KEGGiafu:AF_0206.

Phylogenomic databases

eggNOGiarCOG00676. Archaea.
COG1096. LUCA.
KOiK07573.
OMAiCGNVETR.

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-210-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO30033.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_00975. Exosome_Csl4.
InterProiIPR019495. EXOSC1.
IPR025721. Exosome_cplx_N_dom.
IPR030850. Exosome_Csl4_arc.
IPR012340. NA-bd_OB-fold.
IPR022967. S1_dom.
[Graphical view]
PfamiPF14382. ECR1_N. 1 hit.
PF10447. EXOSC1. 1 hit.
[Graphical view]
SMARTiSM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. "Structural framework for the mechanism of archaeal exosomes in RNA processing."
    Buttner K., Wenig K., Hopfner K.P.
    Mol. Cell 20:461-471(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH RRP41; RRP42 AND ZINC, FUNCTION, SUBUNIT, DOMAIN.
  3. "Quantitative analysis of processive RNA degradation by the archaeal RNA exosome."
    Hartung S., Niederberger T., Hartung M., Tresch A., Hopfner K.P.
    Nucleic Acids Res. 38:5166-5176(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH RRP41; RRP42 AND ZINC, FUNCTION, SUBUNIT.

Entry informationi

Entry nameiCSL4_ARCFU
AccessioniPrimary (citable) accession number: O30033
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 11, 2013
Last sequence update: January 1, 1998
Last modified: May 11, 2016
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The zinc ion has probably a structural role.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. SIMILARITY comments
    Index of protein domains and families

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.