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Protein

Exosome complex component RRP4

Gene

EXOSC2

Organism
Homo sapiens (Human)
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 promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. 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. EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7.1 Publication

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: ProtInc
  • 7S RNA binding Source: ProtInc

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000130713-MONOMER.
ReactomeiR-HSA-380994. ATF4 activates genes.
R-HSA-429958. mRNA decay by 3' to 5' exoribonuclease.
R-HSA-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-HSA-450513. Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
R-HSA-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP4
Alternative name(s):
Exosome component 2
Ribosomal RNA-processing protein 4
Gene namesi
Name:EXOSC2
Synonyms:RRP4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:17097. EXOSC2.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi23404.
OpenTargetsiENSG00000130713.
PharmGKBiPA134876020.

Polymorphism and mutation databases

DMDMi13878748.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000871291 – 293Exosome complex component RRP4Add BLAST293

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei124PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ13868.
MaxQBiQ13868.
PaxDbiQ13868.
PeptideAtlasiQ13868.
PRIDEiQ13868.

PTM databases

iPTMnetiQ13868.
PhosphoSitePlusiQ13868.
SwissPalmiQ13868.

Expressioni

Gene expression databases

BgeeiENSG00000130713.
CleanExiHS_EXOSC2.
ExpressionAtlasiQ13868. baseline and differential.
GenevisibleiQ13868. HS.

Organism-specific databases

HPAiHPA021790.

Interactioni

Subunit structurei

Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms (PubMed:11719186, PubMed:20531389). Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure (PubMed:11719186, PubMed:20531389). Interacts with DIS3 (PubMed:20531389). Interacts with GTPBP1 (PubMed:21515746). Interacts with ZFP36L1 (via N-terminus) (PubMed:15687258).4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DIS3LQ8TF46-12EBI-301735,EBI-3895807
EXOSC3Q9NQT56EBI-301735,EBI-371866
EXOSC4Q9NPD37EBI-301735,EBI-371823
EXOSC7Q150246EBI-301735,EBI-371841
MPHOSPH6Q995473EBI-301735,EBI-373187
ZNF408Q9H9D43EBI-301735,EBI-347633

Protein-protein interaction databases

BioGridi116977. 52 interactors.
DIPiDIP-31264N.
IntActiQ13868. 50 interactors.
MINTiMINT-2633872.
STRINGi9606.ENSP00000361433.

Structurei

Secondary structure

1293
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi45 – 47Combined sources3
Beta strandi49 – 54Combined sources6
Beta strandi56 – 63Combined sources8
Beta strandi66 – 73Combined sources8
Beta strandi80 – 82Combined sources3
Beta strandi86 – 92Combined sources7
Beta strandi95 – 99Combined sources5
Beta strandi101 – 104Combined sources4
Beta strandi106 – 111Combined sources6
Helixi129 – 134Combined sources6
Beta strandi144 – 149Combined sources6
Turni150 – 152Combined sources3
Beta strandi153 – 157Combined sources5
Beta strandi171 – 173Combined sources3
Beta strandi193 – 198Combined sources6
Turni199 – 201Combined sources3
Beta strandi202 – 206Combined sources5
Helixi220 – 222Combined sources3
Helixi228 – 246Combined sources19
Helixi253 – 261Combined sources9
Turni262 – 266Combined sources5
Helixi275 – 289Combined sources15
Turni290 – 292Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35H1-293[»]
ProteinModelPortaliQ13868.
SMRiQ13868.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13868.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini79 – 159S1 motifAdd BLAST81

Sequence similaritiesi

Belongs to the RRP4 family.Curated
Contains 1 S1 motif domain.Curated

Phylogenomic databases

eggNOGiKOG3013. Eukaryota.
COG1097. LUCA.
GeneTreeiENSGT00440000033656.
HOGENOMiHOG000193685.
HOVERGENiHBG051517.
InParanoidiQ13868.
KOiK03679.
OMAiMSTNAAI.
OrthoDBiEOG091G0E3V.
PhylomeDBiQ13868.
TreeFamiTF105623.

Family and domain databases

InterProiIPR025721. Exosome_cplx_N_dom.
IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF14382. ECR1_N. 1 hit.
PF15985. KH_6. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q13868-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAMEMRLPVA RKPLSERLGR DTKKHLVVPG DTITTDTGFM RGHGTYMGEE
60 70 80 90 100
KLIASVAGSV ERVNKLICVK ALKTRYIGEV GDIVVGRITE VQQKRWKVET
110 120 130 140 150
NSRLDSVLLL SSMNLPGGEL RRRSAEDELA MRGFLQEGDL ISAEVQAVFS
160 170 180 190 200
DGAVSLHTRS LKYGKLGQGV LVQVSPSLVK RQKTHFHDLP CGASVILGNN
210 220 230 240 250
GFIWIYPTPE HKEEEAGGFI ANLEPVSLAD REVISRLRNC IISLVTQRMM
260 270 280 290
LYDTSILYCY EASLPHQIKD ILKPEIMEEI VMETRQRLLE QEG
Length:293
Mass (Da):32,789
Last modified:April 27, 2001 - v2
Checksum:i882033F50791643F
GO
Isoform 2 (identifier: Q13868-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     143-168: Missing.

Note: No experimental confirmation available.
Show »
Length:267
Mass (Da):30,045
Checksum:iFCBD02E381F5FAB9
GO
Isoform 3 (identifier: Q13868-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     91-120: Missing.

Show »
Length:263
Mass (Da):29,408
Checksum:iAB9C1DDC75EB79D1
GO

Sequence cautioni

The sequence AAB60392 differs from that shown. Reason: Erroneous gene model prediction.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_05756891 – 120Missing in isoform 3. Add BLAST30
Alternative sequenceiVSP_054921143 – 168Missing in isoform 2. 1 PublicationAdd BLAST26

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U07561 Genomic DNA. Translation: AAB60392.1. Sequence problems.
AK001916 mRNA. Translation: BAA91977.1.
AK022460 mRNA. Translation: BAB14043.1.
AK296605 mRNA. Translation: BAG59218.1.
AL359092 Genomic DNA. Translation: CAM45748.1.
CH471090 Genomic DNA. Translation: EAW87942.1.
CH471090 Genomic DNA. Translation: EAW87944.1.
BC000747 mRNA. Translation: AAH00747.1.
CCDSiCCDS65160.1. [Q13868-2]
CCDS65161.1. [Q13868-3]
CCDS6935.1. [Q13868-1]
RefSeqiNP_001269637.1. NM_001282708.1. [Q13868-2]
NP_001269638.1. NM_001282709.1. [Q13868-3]
NP_055100.2. NM_014285.6. [Q13868-1]
UniGeneiHs.654643.

Genome annotation databases

EnsembliENST00000372351; ENSP00000361426; ENSG00000130713. [Q13868-3]
ENST00000372358; ENSP00000361433; ENSG00000130713. [Q13868-1]
ENST00000546165; ENSP00000444917; ENSG00000130713. [Q13868-2]
GeneIDi23404.
KEGGihsa:23404.
UCSCiuc004bzu.4. human. [Q13868-1]
uc033djg.2. human.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U07561 Genomic DNA. Translation: AAB60392.1. Sequence problems.
AK001916 mRNA. Translation: BAA91977.1.
AK022460 mRNA. Translation: BAB14043.1.
AK296605 mRNA. Translation: BAG59218.1.
AL359092 Genomic DNA. Translation: CAM45748.1.
CH471090 Genomic DNA. Translation: EAW87942.1.
CH471090 Genomic DNA. Translation: EAW87944.1.
BC000747 mRNA. Translation: AAH00747.1.
CCDSiCCDS65160.1. [Q13868-2]
CCDS65161.1. [Q13868-3]
CCDS6935.1. [Q13868-1]
RefSeqiNP_001269637.1. NM_001282708.1. [Q13868-2]
NP_001269638.1. NM_001282709.1. [Q13868-3]
NP_055100.2. NM_014285.6. [Q13868-1]
UniGeneiHs.654643.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35H1-293[»]
ProteinModelPortaliQ13868.
SMRiQ13868.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116977. 52 interactors.
DIPiDIP-31264N.
IntActiQ13868. 50 interactors.
MINTiMINT-2633872.
STRINGi9606.ENSP00000361433.

PTM databases

iPTMnetiQ13868.
PhosphoSitePlusiQ13868.
SwissPalmiQ13868.

Polymorphism and mutation databases

DMDMi13878748.

Proteomic databases

EPDiQ13868.
MaxQBiQ13868.
PaxDbiQ13868.
PeptideAtlasiQ13868.
PRIDEiQ13868.

Protocols and materials databases

DNASUi23404.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000372351; ENSP00000361426; ENSG00000130713. [Q13868-3]
ENST00000372358; ENSP00000361433; ENSG00000130713. [Q13868-1]
ENST00000546165; ENSP00000444917; ENSG00000130713. [Q13868-2]
GeneIDi23404.
KEGGihsa:23404.
UCSCiuc004bzu.4. human. [Q13868-1]
uc033djg.2. human.

Organism-specific databases

CTDi23404.
DisGeNETi23404.
GeneCardsiEXOSC2.
H-InvDBHIX0008473.
HGNCiHGNC:17097. EXOSC2.
HPAiHPA021790.
MIMi602238. gene.
neXtProtiNX_Q13868.
OpenTargetsiENSG00000130713.
PharmGKBiPA134876020.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3013. Eukaryota.
COG1097. LUCA.
GeneTreeiENSGT00440000033656.
HOGENOMiHOG000193685.
HOVERGENiHBG051517.
InParanoidiQ13868.
KOiK03679.
OMAiMSTNAAI.
OrthoDBiEOG091G0E3V.
PhylomeDBiQ13868.
TreeFamiTF105623.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000130713-MONOMER.
ReactomeiR-HSA-380994. ATF4 activates genes.
R-HSA-429958. mRNA decay by 3' to 5' exoribonuclease.
R-HSA-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-HSA-450513. Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
R-HSA-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

ChiTaRSiEXOSC2. human.
EvolutionaryTraceiQ13868.
GeneWikiiExosome_component_2.
GenomeRNAii23404.
PROiQ13868.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000130713.
CleanExiHS_EXOSC2.
ExpressionAtlasiQ13868. baseline and differential.
GenevisibleiQ13868. HS.

Family and domain databases

InterProiIPR025721. Exosome_cplx_N_dom.
IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF14382. ECR1_N. 1 hit.
PF15985. KH_6. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiEXOS2_HUMAN
AccessioniPrimary (citable) accession number: Q13868
Secondary accession number(s): A3KFL3
, A3KFL4, B4DKK6, Q9NUY4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: April 27, 2001
Last modified: November 2, 2016
This is version 167 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.