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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

Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

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.

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

HGNCiHGNC:17944. EXOSC3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytoplasmic exosome (RNase complex) Source: UniProtKB
  • cytosol Source: Reactome
  • exosome (RNase complex) Source: UniProtKB
  • nuclear exosome (RNase complex) Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • transcriptionally active chromatin Source: UniProtKB
Complete GO annotation...

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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti31 – 311G → A in PCH1B. 1 Publication
Corresponds to variant rs387907196 [ dbSNP | Ensembl ].
VAR_068505
Natural varianti132 – 1321D → A in PCH1B. 1 Publication
Corresponds to variant rs141138948 [ dbSNP | Ensembl ].
VAR_068506
Natural varianti139 – 1391A → P in PCH1B. 1 Publication
Corresponds to variant rs387907195 [ dbSNP | Ensembl ].
VAR_068507
Natural varianti238 – 2381W → R in PCH1B. 1 Publication
Corresponds to variant rs672601332 [ dbSNP | Ensembl ].
VAR_068508

Keywords - Diseasei

Disease mutation, Neurodegeneration

Organism-specific databases

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

Polymorphism and mutation databases

BioMutaiEXOSC3.
DMDMi14285758.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources1 Publication
Chaini2 – 275274Exosome complex component RRP40PRO_0000087131Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineCombined sources1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9NQT5.
MaxQBiQ9NQT5.
PaxDbiQ9NQT5.
PeptideAtlasiQ9NQT5.
PRIDEiQ9NQT5.

PTM databases

iPTMnetiQ9NQT5.
PhosphoSiteiQ9NQT5.

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

WithEntry#Exp.IntActNotes
DIS3Q9Y2L13EBI-371866,EBI-373539
DIS3LQ8TF464EBI-371866,EBI-3672244
EXOSC2Q138686EBI-371866,EBI-301735
EXOSC4Q9NPD35EBI-371866,EBI-371823
EXOSC5Q9NQT48EBI-371866,EBI-371876
EXOSC8Q96B263EBI-371866,EBI-371922

Protein-protein interaction databases

BioGridi119217. 29 interactions.
DIPiDIP-29847N.
IntActiQ9NQT5. 23 interactions.
MINTiMINT-3072286.
STRINGi9606.ENSP00000323046.

Structurei

Secondary structure

1
275
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi22 – 243Combined sources
Beta strandi25 – 273Combined sources
Beta strandi30 – 345Combined sources
Beta strandi45 – 495Combined sources
Beta strandi78 – 803Combined sources
Beta strandi85 – 895Combined sources
Turni92 – 943Combined sources
Beta strandi99 – 1035Combined sources
Beta strandi113 – 12513Combined sources
Beta strandi128 – 1325Combined sources
Beta strandi134 – 1374Combined sources
Beta strandi141 – 1433Combined sources
Beta strandi145 – 1473Combined sources
Beta strandi153 – 1575Combined sources
Beta strandi162 – 1698Combined sources
Beta strandi177 – 1793Combined sources
Turni183 – 1853Combined sources
Beta strandi198 – 2003Combined sources
Helixi204 – 2118Combined sources
Helixi217 – 2204Combined sources
Beta strandi224 – 2263Combined sources
Beta strandi230 – 2323Combined sources
Turni233 – 2353Combined sources
Beta strandi236 – 2394Combined sources
Helixi244 – 25613Combined sources
Turni262 – 2643Combined sources
Helixi265 – 27410Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35G1-275[»]
ProteinModelPortaliQ9NQT5.
SMRiQ9NQT5. Positions 17-275.
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.
OMAiHKEPGSG.
OrthoDBiEOG091G0Q58.
PhylomeDBiQ9NQT5.
TreeFamiTF314927.

Family and domain databases

InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 2 hits.
PfamiPF15985. KH_6. 1 hit.
[Graphical view]
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti56 – 6510NARACSRVRV → MLERARGCAF in AAD34097 (PubMed:10810093).Curated
Sequence conflicti95 – 951S → G in AAD34097 (PubMed:10810093).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti31 – 311G → A in PCH1B. 1 Publication
Corresponds to variant rs387907196 [ dbSNP | Ensembl ].
VAR_068505
Natural varianti80 – 801V → F.1 Publication
Corresponds to variant rs374550999 [ dbSNP | Ensembl ].
VAR_074169
Natural varianti132 – 1321D → A in PCH1B. 1 Publication
Corresponds to variant rs141138948 [ dbSNP | Ensembl ].
VAR_068506
Natural varianti139 – 1391A → P in PCH1B. 1 Publication
Corresponds to variant rs387907195 [ dbSNP | Ensembl ].
VAR_068507
Natural varianti225 – 2251Y → H.
Corresponds to variant rs3208406 [ dbSNP | Ensembl ].
VAR_054098
Natural varianti238 – 2381W → R in PCH1B. 1 Publication
Corresponds to variant rs672601332 [ dbSNP | Ensembl ].
VAR_068508

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei159 – 275117VGDLI…RLAES → AISSRL in isoform 2. 1 PublicationVSP_043457Add
BLAST

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. Translation: CAI13880.1.
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

Cross-referencesi

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. Translation: CAI13880.1.
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35G1-275[»]
ProteinModelPortaliQ9NQT5.
SMRiQ9NQT5. Positions 17-275.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119217. 29 interactions.
DIPiDIP-29847N.
IntActiQ9NQT5. 23 interactions.
MINTiMINT-3072286.
STRINGi9606.ENSP00000323046.

PTM databases

iPTMnetiQ9NQT5.
PhosphoSiteiQ9NQT5.

Polymorphism and mutation databases

BioMutaiEXOSC3.
DMDMi14285758.

Proteomic databases

EPDiQ9NQT5.
MaxQBiQ9NQT5.
PaxDbiQ9NQT5.
PeptideAtlasiQ9NQT5.
PRIDEiQ9NQT5.

Protocols and materials databases

DNASUi51010.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi51010.
GeneCardsiEXOSC3.
HGNCiHGNC:17944. EXOSC3.
HPAiHPA020485.
MalaCardsiEXOSC3.
MIMi606489. gene.
614678. phenotype.
neXtProtiNX_Q9NQT5.
Orphaneti2254. Pontocerebellar hypoplasia type 1.
PharmGKBiPA134926550.
GenAtlasiSearch...

Phylogenomic databases

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

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.

Miscellaneous databases

EvolutionaryTraceiQ9NQT5.
GeneWikiiExosome_component_3.
GenomeRNAii51010.
PROiQ9NQT5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000107371.
CleanExiHS_EXOSC3.
GenevisibleiQ9NQT5. HS.

Family and domain databases

InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 2 hits.
PfamiPF15985. KH_6. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiEXOS3_HUMAN
AccessioniPrimary (citable) accession number: Q9NQT5
Secondary accession number(s): A8K0K6, Q5QP85, Q9Y3A8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 157 of the entry and version 3 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, 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

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.