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Protein

Exosome complex component RRP4

Gene

EXOSC2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionRNA-binding
Biological processrRNA processing

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000130713.15
HGNCiHGNC:17097 EXOSC2
MIMi602238 gene
neXtProtiNX_Q13868

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi23404
MalaCardsiEXOSC2
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
ProteomicsDBi59704

PTM databases

iPTMnetiQ13868
PhosphoSitePlusiQ13868
SwissPalmiQ13868

Expressioni

Gene expression databases

BgeeiENSG00000130713
CleanExiHS_EXOSC2
ExpressionAtlasiQ13868 baseline and differential
GenevisibleiQ13868 HS

Organism-specific databases

HPAiHPA021756
HPA021790

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

Show more details

Protein-protein interaction databases

BioGridi116977, 59 interactors
ComplexPortaliCPX-476 Nuclear exosome complex, DIS3-EXOSC10 variant
CPX-591 Nucleolar exosome complex, EXOSC10 variant
CPX-592 Cytoplasmic exosome complex, DIS3L variant
CPX-593 Exosome complex, DIS3 variant
CPX-600 Cytoplasmic exosome complex, DIS3L-EXOSC10 variant
CORUMiQ13868
DIPiDIP-31264N
IntActiQ13868, 51 interactors
MINTiQ13868
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
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

Phylogenomic databases

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

Family and domain databases

InterProiView protein in InterPro
IPR025721 Exosome_cplx_N_dom
IPR026699 Exosome_RNA_bind1/RRP40/RRP4
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR012340 NA-bd_OB-fold
PANTHERiPTHR21321 PTHR21321, 1 hit
PfamiView protein in Pfam
PF14382 ECR1_N, 1 hit
PF15985 KH_6, 1 hit
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 No translation available.
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

Similar proteinsi

Entry informationi

Entry nameiEXOS2_HUMAN
AccessioniPrimary (citable) accession number: Q13868
Secondary accession number(s): A3KFL3
, A3KFL4, B4DKK6, Q9NUY4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: April 27, 2001
Last modified: June 20, 2018
This is version 178 of the entry and version 2 of the sequence. See 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

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