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Protein

Exosome complex component Rrp4

Gene

rrp4

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. Confers strong poly(A) specificity to the exosome (Probable).2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-505-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Rrp4UniRule annotation
Gene namesi
Name:rrp4UniRule annotation
Ordered Locus Names:AF_0492
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 – 223223Exosome complex component Rrp4PRO_0000050145Add
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.UniRule annotation2 Publications

Protein-protein interaction databases

STRINGi224325.AF0492.

Structurei

Secondary structure

1
223
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 134Combined sources
Beta strandi22 – 254Combined sources
Beta strandi28 – 314Combined sources
Beta strandi33 – 397Combined sources
Beta strandi44 – 485Combined sources
Beta strandi50 – 523Combined sources
Beta strandi60 – 689Combined sources
Beta strandi70 – 767Combined sources
Beta strandi78 – 814Combined sources
Beta strandi83 – 864Combined sources
Helixi87 – 893Combined sources
Helixi99 – 1013Combined sources
Beta strandi108 – 1169Combined sources
Beta strandi122 – 1254Combined sources
Beta strandi128 – 1303Combined sources
Beta strandi132 – 14110Combined sources
Helixi144 – 1463Combined sources
Helixi147 – 1515Combined sources
Helixi153 – 1553Combined sources
Helixi156 – 16510Combined sources
Beta strandi168 – 1714Combined sources
Beta strandi175 – 1817Combined sources
Helixi183 – 19816Combined sources
Helixi205 – 21814Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BA0X-ray2.70A/B/C1-223[»]
ProteinModelPortaliO29758.
SMRiO29758. Positions 2-223.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29758.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini58 – 12770S1 motifUniRule annotationAdd
BLAST
Domaini135 – 19359KHUniRule annotationAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the RRP4 family.UniRule annotation
Contains 1 KH domain.UniRule annotation
Contains 1 S1 motif domain.UniRule annotation

Phylogenomic databases

eggNOGiarCOG00678. Archaea.
COG1097. LUCA.
KOiK03679.
OMAiPYDGLLH.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.30.1370.10. 1 hit.
HAMAPiMF_00623. Exosome_Rrp4. 1 hit.
InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR023474. Rrp4.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF00013. KH_1. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTiSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
PROSITEiPS50084. KH_TYPE_1. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O29758-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRKIVLPGDL LSTNPRAAGY GTYVEGGKVY AKIIGLFDQT ETHVRVIPLK
60 70 80 90 100
GRYTPSVGDV VIGIIREVAA NGWAVDIYSP YQAFLPVSEN PEMKPNKKPN
110 120 130 140 150
EVLDIGDAII AKVLNIDPKM KVTLTMKDRI CRPIRFGRIV AINPARVPRV
160 170 180 190 200
IGKKGSMIKL LKSELDVQIV VGQNGLIWVN GDRRKVSIAE EAIYLIEQEA
210 220
HTEGLTDRVA EFIKRRKADV GIQ
Length:223
Mass (Da):24,725
Last modified:January 1, 1998 - v1
Checksum:iA11B7F1A26972833
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90745.1.
PIRiD69311.
RefSeqiWP_010877999.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90745; AAB90745; AF_0492.
GeneIDi24794032.
KEGGiafu:AF_0492.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90745.1.
PIRiD69311.
RefSeqiWP_010877999.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BA0X-ray2.70A/B/C1-223[»]
ProteinModelPortaliO29758.
SMRiO29758. Positions 2-223.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0492.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90745; AAB90745; AF_0492.
GeneIDi24794032.
KEGGiafu:AF_0492.

Phylogenomic databases

eggNOGiarCOG00678. Archaea.
COG1097. LUCA.
KOiK03679.
OMAiPYDGLLH.

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-505-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO29758.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.30.1370.10. 1 hit.
HAMAPiMF_00623. Exosome_Rrp4. 1 hit.
InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR023474. Rrp4.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF00013. KH_1. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTiSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
PROSITEiPS50084. KH_TYPE_1. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRRP4_ARCFU
AccessioniPrimary (citable) accession number: O29758
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: January 1, 1998
Last modified: September 7, 2016
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.