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UniProtKB - Q9NPD3 (EXOS4_HUMAN)

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Protein

Exosome complex component RRP41

Gene

EXOSC4

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. EXOSC4 binds to ARE-containing RNAs.5 Publications

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: UniProtKB
  • AU-rich element binding Source: UniProtKB
View the complete GO annotation on QuickGO ...

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: Reactome
  • U4 snRNA 3'-end processing Source: GO_Central
View the complete GO annotation on QuickGO ...

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 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

EuPathDBiHostDB:ENSG00000178896.6.
HGNCiHGNC:18189. EXOSC4.
MIMi606491. gene.
neXtProtiNX_Q9NPD3.

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

OpenTargetsiENSG00000178896.
PharmGKBiPA134867931.

Polymorphism and mutation databases

BioMutaiEXOSC4.
DMDMi14285756.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00001399582 – 245Exosome complex component RRP41Add BLAST244

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9NPD3.
MaxQBiQ9NPD3.
PaxDbiQ9NPD3.
PeptideAtlasiQ9NPD3.
PRIDEiQ9NPD3.

2D gel databases

SWISS-2DPAGEiQ9NPD3.

PTM databases

iPTMnetiQ9NPD3.
PhosphoSitePlusiQ9NPD3.

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

Show more details

Protein-protein interaction databases

BioGridi120007. 95 interactors.
CORUMiQ9NPD3.
DIPiDIP-31165N.
IntActiQ9NPD3. 69 interactors.
MINTiQ9NPD3.
STRINGi9606.ENSP00000315476.

Structurei

Secondary structure

1245
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 17Combined sources4
Beta strandi25 – 30Combined sources6
Beta strandi32 – 45Combined sources14
Beta strandi47 – 57Combined sources11
Beta strandi60 – 62Combined sources3
Beta strandi72 – 78Combined sources7
Turni80 – 82Combined sources3
Beta strandi83 – 85Combined sources3
Turni89 – 91Combined sources3
Helixi94 – 109Combined sources16
Helixi113 – 115Combined sources3
Beta strandi119 – 129Combined sources11
Helixi134 – 148Combined sources15
Beta strandi158 – 165Combined sources8
Beta strandi168 – 172Combined sources5
Helixi175 – 178Combined sources4
Beta strandi185 – 189Combined sources5
Turni191 – 193Combined sources3
Beta strandi198 – 201Combined sources4
Helixi210 – 239Combined sources30

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35B2-245[»]
ProteinModelPortaliQ9NPD3.
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.
OMAiVINCQYS.
PhylomeDBiQ9NPD3.
TreeFamiTF313915.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiView protein in InterPro
IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR036345. ExoRNase_PH_dom2_sf.
IPR027408. PNPase/RNase_PH_dom_sf.
IPR020568. Ribosomal_S5_D2-typ_fold.
PfamiView protein in Pfam
PF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
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.

Similar proteinsi

Entry informationi

Entry nameiEXOS4_HUMAN
AccessioniPrimary (citable) accession number: Q9NPD3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: January 23, 2007
Last modified: March 28, 2018
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

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