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Protein

Exosome complex component RRP40

Gene

EXOSC3

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. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5.4 Publications

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: UniProtKB
  • RNA binding Source: GO_Central

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 RRP40
Alternative name(s):
Exosome component 3
Ribosomal RNA-processing protein 40
p10
Gene namesi
Name:EXOSC3
Synonyms:RRP40
ORF Names:CGI-102
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

EuPathDBiHostDB:ENSG00000107371.12.
HGNCiHGNC:17944. EXOSC3.

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

Involvement in diseasei

Pontocerebellar hypoplasia 1B (PCH1B)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA severe autosomal recessive neurologic disorder characterized by a combination of cerebellar and spinal motor neuron degeneration beginning at birth. There is diffuse muscle weakness, progressive microcephaly, global developmental delay, and brainstem involvement.
See also OMIM:614678
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06850531G → A in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs387907196Ensembl.1
Natural variantiVAR_068506132D → A in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs141138948Ensembl.1
Natural variantiVAR_068507139A → P in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs387907195Ensembl.1
Natural variantiVAR_068508238W → R in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs672601332Ensembl.1

Keywords - Diseasei

Disease mutation, Neurodegeneration

Organism-specific databases

DisGeNETi51010.
MalaCardsiEXOSC3.
MIMi614678. phenotype.
OpenTargetsiENSG00000107371.
Orphaneti2254. Pontocerebellar hypoplasia type 1.
PharmGKBiPA134926550.

Polymorphism and mutation databases

BioMutaiEXOSC3.
DMDMi14285758.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00000871312 – 275Exosome complex component RRP40Add BLAST274

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1 Publication1
Cross-linki151Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ9NQT5.
MaxQBiQ9NQT5.
PaxDbiQ9NQT5.
PeptideAtlasiQ9NQT5.
PRIDEiQ9NQT5.

PTM databases

iPTMnetiQ9NQT5.
PhosphoSitePlusiQ9NQT5.

Expressioni

Gene expression databases

BgeeiENSG00000107371.
CleanExiHS_EXOSC3.
GenevisibleiQ9NQT5. HS.

Organism-specific databases

HPAiHPA020485.

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. 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. Interacts with GTPBP1. Interacts with ZC3HAV1. Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner.5 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi119217. 31 interactors.
CORUMiQ9NQT5.
DIPiDIP-29847N.
IntActiQ9NQT5. 26 interactors.
MINTiMINT-3072286.
STRINGi9606.ENSP00000323046.

Structurei

Secondary structure

1275
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi22 – 24Combined sources3
Beta strandi25 – 27Combined sources3
Beta strandi30 – 34Combined sources5
Beta strandi45 – 49Combined sources5
Beta strandi78 – 80Combined sources3
Beta strandi85 – 89Combined sources5
Turni92 – 94Combined sources3
Beta strandi99 – 103Combined sources5
Beta strandi113 – 125Combined sources13
Beta strandi128 – 132Combined sources5
Beta strandi134 – 137Combined sources4
Beta strandi141 – 143Combined sources3
Beta strandi145 – 147Combined sources3
Beta strandi153 – 157Combined sources5
Beta strandi162 – 169Combined sources8
Beta strandi177 – 179Combined sources3
Turni183 – 185Combined sources3
Beta strandi198 – 200Combined sources3
Helixi204 – 211Combined sources8
Helixi217 – 220Combined sources4
Beta strandi224 – 226Combined sources3
Beta strandi230 – 232Combined sources3
Turni233 – 235Combined sources3
Beta strandi236 – 239Combined sources4
Helixi244 – 256Combined sources13
Turni262 – 264Combined sources3
Helixi265 – 274Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35G1-275[»]
ProteinModelPortaliQ9NQT5.
SMRiQ9NQT5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NQT5.

Family & Domainsi

Sequence similaritiesi

Belongs to the RRP40 family.Curated

Phylogenomic databases

eggNOGiKOG1004. Eukaryota.
COG1097. LUCA.
GeneTreeiENSGT00390000012042.
HOGENOMiHOG000012998.
HOVERGENiHBG051518.
InParanoidiQ9NQT5.
KOiK03681.
OMAiISYLAFE.
OrthoDBiEOG091G0Q58.
PhylomeDBiQ9NQT5.
TreeFamiTF314927.

Family and domain databases

InterProiView protein in InterPro
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
PF15985. KH_6. 1 hit.
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NQT5-1) [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
MAEPASVAAE SLAGSRARAA RTVLGQVVLP GEELLLPEQE DAEGPGGAVE
60 70 80 90 100
RPLSLNARAC SRVRVVCGPG LRRCGDRLLV TKCGRLRHKE PGSGSGGGVY
110 120 130 140 150
WVDSQQKRYV PVKGDHVIGI VTAKSGDIFK VDVGGSEPAS LSYLSFEGAT
160 170 180 190 200
KRNRPNVQVG DLIYGQFVVA NKDMEPEMVC IDSCGRANGM GVIGQDGLLF
210 220 230 240 250
KVTLGLIRKL LAPDCEIIQE VGKLYPLEIV FGMNGRIWVK AKTIQQTLIL
260 270
ANILEACEHM TSDQRKQIFS RLAES
Length:275
Mass (Da):29,572
Last modified:January 23, 2007 - v3
Checksum:i264322144A199166
GO
Isoform 2 (identifier: Q9NQT5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     159-275: VGDLIYGQFV...KQIFSRLAES → AISSRL

Note: No experimental confirmation available.
Show »
Length:164
Mass (Da):17,248
Checksum:i51C07B44337D0076
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti56 – 65NARACSRVRV → MLERARGCAF in AAD34097 (PubMed:10810093).Curated10
Sequence conflicti95S → G in AAD34097 (PubMed:10810093).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06850531G → A in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs387907196Ensembl.1
Natural variantiVAR_07416980V → F1 PublicationCorresponds to variant dbSNP:rs374550999Ensembl.1
Natural variantiVAR_068506132D → A in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs141138948Ensembl.1
Natural variantiVAR_068507139A → P in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs387907195Ensembl.1
Natural variantiVAR_054098225Y → H. Corresponds to variant dbSNP:rs3208406Ensembl.1
Natural variantiVAR_068508238W → R in PCH1B. 1 PublicationCorresponds to variant dbSNP:rs672601332Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_043457159 – 275VGDLI…RLAES → AISSRL in isoform 2. 1 PublicationAdd BLAST117

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281132 mRNA. Translation: AAF82133.1.
AK289571 mRNA. Translation: BAF82260.1.
AK290864 mRNA. Translation: BAF83553.1.
AL138752 Genomic DNA. No translation available.
CH471071 Genomic DNA. Translation: EAW58264.1.
BC002437 mRNA. Translation: AAH02437.1.
BC008880 mRNA. Translation: AAH08880.1.
AF151860 mRNA. Translation: AAD34097.1.
CCDSiCCDS35016.1. [Q9NQT5-1]
CCDS43805.1. [Q9NQT5-2]
RefSeqiNP_001002269.1. NM_001002269.2. [Q9NQT5-2]
NP_057126.2. NM_016042.3. [Q9NQT5-1]
UniGeneiHs.602571.
Hs.713483.

Genome annotation databases

EnsembliENST00000327304; ENSP00000323046; ENSG00000107371. [Q9NQT5-1]
ENST00000396521; ENSP00000379775; ENSG00000107371. [Q9NQT5-2]
ENST00000465229; ENSP00000418422; ENSG00000107371. [Q9NQT5-2]
GeneIDi51010.
KEGGihsa:51010.
UCSCiuc004aal.4. human. [Q9NQT5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiEXOS3_HUMAN
AccessioniPrimary (citable) accession number: Q9NQT5
Secondary accession number(s): A8K0K6, Q5QP85, Q9Y3A8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: January 23, 2007
Last modified: October 25, 2017
This is version 165 of the entry and version 3 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families