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UniProtKB - Q9NPD3 (EXOS4_HUMAN)

UniProt

Q9NPD3 - EXOS4_HUMAN

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Protein

Exosome complex component RRP41

Gene

EXOSC4

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. EXOSC4 binds to ARE-containing RNAs.5 Publications

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: UniProtKB
  • AU-rich element binding Source: UniProtKB

GO - Biological processi

  • defense response to virus Source: MGI
  • DNA deamination Source: UniProtKB
  • exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
  • histone mRNA catabolic process Source: UniProtKB
  • maturation of 5.8S rRNA Source: UniProtKB
  • nuclear mRNA surveillance Source: UniProtKB
  • nuclear-transcribed mRNA catabolic process Source: UniProtKB
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: GO_Central
  • polyadenylation-dependent snoRNA 3'-end processing Source: GO_Central
  • positive regulation of cell growth Source: UniProtKB
  • regulation of mRNA stability Source: Reactome
  • rRNA 3'-end processing Source: GO_Central
  • rRNA catabolic process Source: GO_Central
  • rRNA processing Source: UniProtKB
  • U4 snRNA 3'-end processing Source: GO_Central
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 RRP41
Alternative name(s):
Exosome component 4
Ribosomal RNA-processing protein 41
p12A
Gene namesi
Name:EXOSC4
Synonyms:RRP41, SKI6
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 8

Organism-specific databases

HGNCiHGNC:18189. EXOSC4.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleus › nucleolus 1 Publication
  • Nucleus 1 Publication

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
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • transcriptionally active chromatin Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134867931.

Polymorphism and mutation databases

BioMutaiEXOSC4.
DMDMi14285756.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources1 Publication
Chaini2 – 245244Exosome complex component RRP41PRO_0000139958Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9NPD3.
MaxQBiQ9NPD3.
PaxDbiQ9NPD3.
PeptideAtlasiQ9NPD3.
PRIDEiQ9NPD3.

2D gel databases

SWISS-2DPAGEQ9NPD3.

PTM databases

iPTMnetiQ9NPD3.
PhosphoSiteiQ9NPD3.

Expressioni

Gene expression databases

BgeeiENSG00000178896.
CleanExiHS_EXOSC4.
ExpressionAtlasiQ9NPD3. baseline and differential.
GenevisibleiQ9NPD3. HS.

Organism-specific databases

HPAiHPA024792.

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 DDX60.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EXOSC1Q9Y3B26EBI-371823,EBI-371892
EXOSC10Q017804EBI-371823,EBI-358236
EXOSC2Q138687EBI-371823,EBI-301735
EXOSC3Q9NQT55EBI-371823,EBI-371866
EXOSC7Q150244EBI-371823,EBI-371841
EXOSC9Q062655EBI-371823,EBI-347966

Protein-protein interaction databases

BioGridi120007. 86 interactions.
DIPiDIP-31165N.
IntActiQ9NPD3. 60 interactions.
MINTiMINT-2818708.
STRINGi9606.ENSP00000315476.

Structurei

Secondary structure

1
245
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi14 – 174Combined sources
Beta strandi25 – 306Combined sources
Beta strandi32 – 4514Combined sources
Beta strandi47 – 5711Combined sources
Beta strandi60 – 623Combined sources
Beta strandi72 – 787Combined sources
Turni80 – 823Combined sources
Beta strandi83 – 853Combined sources
Turni89 – 913Combined sources
Helixi94 – 10916Combined sources
Helixi113 – 1153Combined sources
Beta strandi119 – 12911Combined sources
Helixi134 – 14815Combined sources
Beta strandi158 – 1658Combined sources
Beta strandi168 – 1725Combined sources
Helixi175 – 1784Combined sources
Beta strandi185 – 1895Combined sources
Turni191 – 1933Combined sources
Beta strandi198 – 2014Combined sources
Helixi210 – 23930Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35B2-245[»]
ProteinModelPortaliQ9NPD3.
SMRiQ9NPD3. Positions 7-241.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NPD3.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiKOG1068. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG051519.
InParanoidiQ9NPD3.
KOiK11600.
OMAiDITLLQM.
PhylomeDBiQ9NPD3.
TreeFamiTF313915.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9NPD3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGLELLSDQ GYRVDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA 
        60         70         80         90        100
VVYGPHEIRG SRARALPDRA LVNCQYSSAT FSTGERKRRP HGDRKSCEMG 
       110        120        130        140        150
LQLRQTFEAA ILTQLHPRSQ IDIYVQVLQA DGGTYAACVN AATLAVLDAG 
       160        170        180        190        200
IPMRDFVCAC SAGFVDGTAL ADLSHVEEAA GGPQLALALL PASGQIALLE 
       210        220        230        240 
MDARLHEDHL ERVLEAAAQA ARDVHTLLDR VVRQHVREAS ILLGD
Length:245
Mass (Da):26,383
Last modified:January 23, 2007 - v3
Checksum:i7A24E97897DAF313
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281133 mRNA. Translation: AAF82134.1.
AK000598 mRNA. Translation: BAA91279.1.
AC109322 Genomic DNA. No translation available.
BC002777 mRNA. Translation: AAH02777.1.
CCDSiCCDS6414.1.
RefSeqiNP_061910.1. NM_019037.2.
UniGeneiHs.632041.

Genome annotation databases

EnsembliENST00000316052; ENSP00000315476; ENSG00000178896.
GeneIDi54512.
KEGGihsa:54512.
UCSCiuc003zau.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281133 mRNA. Translation: AAF82134.1.
AK000598 mRNA. Translation: BAA91279.1.
AC109322 Genomic DNA. No translation available.
BC002777 mRNA. Translation: AAH02777.1.
CCDSiCCDS6414.1.
RefSeqiNP_061910.1. NM_019037.2.
UniGeneiHs.632041.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35B2-245[»]
ProteinModelPortaliQ9NPD3.
SMRiQ9NPD3. Positions 7-241.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120007. 86 interactions.
DIPiDIP-31165N.
IntActiQ9NPD3. 60 interactions.
MINTiMINT-2818708.
STRINGi9606.ENSP00000315476.

PTM databases

iPTMnetiQ9NPD3.
PhosphoSiteiQ9NPD3.

Polymorphism and mutation databases

BioMutaiEXOSC4.
DMDMi14285756.

2D gel databases

SWISS-2DPAGEQ9NPD3.

Proteomic databases

EPDiQ9NPD3.
MaxQBiQ9NPD3.
PaxDbiQ9NPD3.
PeptideAtlasiQ9NPD3.
PRIDEiQ9NPD3.

Protocols and materials databases

DNASUi54512.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000316052; ENSP00000315476; ENSG00000178896.
GeneIDi54512.
KEGGihsa:54512.
UCSCiuc003zau.4. human.

Organism-specific databases

CTDi54512.
GeneCardsiEXOSC4.
HGNCiHGNC:18189. EXOSC4.
HPAiHPA024792.
MIMi606491. gene.
neXtProtiNX_Q9NPD3.
PharmGKBiPA134867931.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1068. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG051519.
InParanoidiQ9NPD3.
KOiK11600.
OMAiDITLLQM.
PhylomeDBiQ9NPD3.
TreeFamiTF313915.

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

EvolutionaryTraceiQ9NPD3.
GeneWikiiExosome_component_4.
GenomeRNAii54512.
PROiQ9NPD3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000178896.
CleanExiHS_EXOSC4.
ExpressionAtlasiQ9NPD3. baseline and differential.
GenevisibleiQ9NPD3. HS.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiEXOS4_HUMAN
AccessioniPrimary (citable) accession number: Q9NPD3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 152 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

Caution

The six exosome core subunits containing a RNase PH-domain are not phosphorolytically active.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 8
    Human chromosome 8: 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.