UniProtKB - Q9NPD3 (EXOS4_HUMAN)
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Protein
Exosome complex component RRP41
Gene
EXOSC4
Organism
Homo sapiens (Human)
Status
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: Reactome
- U4 snRNA 3'-end processing Source: GO_Central
Keywordsi
Molecular function | RNA-binding |
Biological process | rRNA processing |
Enzyme and pathway databases
Reactomei | R-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 RRP41Alternative name(s): Exosome component 4 Ribosomal RNA-processing protein 41 p12A |
Gene namesi | Name:EXOSC4 Synonyms:RRP41, SKI6 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000178896.6. |
HGNCi | HGNC:18189. EXOSC4. |
MIMi | 606491. gene. |
neXtProti | NX_Q9NPD3. |
Pathology & Biotechi
Organism-specific databases
OpenTargetsi | ENSG00000178896. |
PharmGKBi | PA134867931. |
Polymorphism and mutation databases
BioMutai | EXOSC4. |
DMDMi | 14285756. |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedCombined sources1 Publication | |||
ChainiPRO_0000139958 | 2 – 245 | Exosome complex component RRP41Add BLAST | 244 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylalanineCombined sources1 Publication | 1 |
Keywords - PTMi
AcetylationProteomic databases
EPDi | Q9NPD3. |
MaxQBi | Q9NPD3. |
PaxDbi | Q9NPD3. |
PeptideAtlasi | Q9NPD3. |
PRIDEi | Q9NPD3. |
2D gel databases
SWISS-2DPAGEi | Q9NPD3. |
PTM databases
iPTMneti | Q9NPD3. |
PhosphoSitePlusi | Q9NPD3. |
Expressioni
Gene expression databases
Bgeei | ENSG00000178896. |
CleanExi | HS_EXOSC4. |
ExpressionAtlasi | Q9NPD3. baseline and differential. |
Genevisiblei | Q9NPD3. HS. |
Organism-specific databases
HPAi | HPA024792. |
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
Protein-protein interaction databases
BioGridi | 120007. 95 interactors. |
CORUMi | Q9NPD3. |
DIPi | DIP-31165N. |
IntActi | Q9NPD3. 69 interactors. |
MINTi | Q9NPD3. |
STRINGi | 9606.ENSP00000315476. |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more detailsFeature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Beta strandi | 14 – 17 | Combined sources | 4 | |
Beta strandi | 25 – 30 | Combined sources | 6 | |
Beta strandi | 32 – 45 | Combined sources | 14 | |
Beta strandi | 47 – 57 | Combined sources | 11 | |
Beta strandi | 60 – 62 | Combined sources | 3 | |
Beta strandi | 72 – 78 | Combined sources | 7 | |
Turni | 80 – 82 | Combined sources | 3 | |
Beta strandi | 83 – 85 | Combined sources | 3 | |
Turni | 89 – 91 | Combined sources | 3 | |
Helixi | 94 – 109 | Combined sources | 16 | |
Helixi | 113 – 115 | Combined sources | 3 | |
Beta strandi | 119 – 129 | Combined sources | 11 | |
Helixi | 134 – 148 | Combined sources | 15 | |
Beta strandi | 158 – 165 | Combined sources | 8 | |
Beta strandi | 168 – 172 | Combined sources | 5 | |
Helixi | 175 – 178 | Combined sources | 4 | |
Beta strandi | 185 – 189 | Combined sources | 5 | |
Turni | 191 – 193 | Combined sources | 3 | |
Beta strandi | 198 – 201 | Combined sources | 4 | |
Helixi | 210 – 239 | Combined sources | 30 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2NN6 | X-ray | 3.35 | B | 2-245 | [»] | |
ProteinModelPortali | Q9NPD3. | |||||
ModBasei | Search... | |||||
MobiDBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9NPD3. |
Family & Domainsi
Sequence similaritiesi
Belongs to the RNase PH family.Curated
Phylogenomic databases
eggNOGi | KOG1068. Eukaryota. COG0689. LUCA. |
GeneTreei | ENSGT00550000074804. |
HOGENOMi | HOG000229515. |
HOVERGENi | HBG051519. |
InParanoidi | Q9NPD3. |
KOi | K11600. |
OMAi | VINCQYS. |
PhylomeDBi | Q9NPD3. |
TreeFami | TF313915. |
Family and domain databases
Gene3Di | 3.30.230.70. 1 hit. |
InterProi | View 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. |
Pfami | View protein in Pfam PF01138. RNase_PH. 1 hit. PF03725. RNase_PH_C. 1 hit. |
SUPFAMi | SSF54211. SSF54211. 1 hit. SSF55666. SSF55666. 1 hit. |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
Q9NPD3-1 [UniParc]FASTAAdd to basket
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
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. |
CCDSi | CCDS6414.1. |
RefSeqi | NP_061910.1. NM_019037.2. |
UniGenei | Hs.632041. |
Genome annotation databases
Ensembli | ENST00000316052; ENSP00000315476; ENSG00000178896. |
GeneIDi | 54512. |
KEGGi | hsa:54512. |
UCSCi | uc003zau.4. human. |
Similar proteinsi
Entry informationi
Entry namei | EXOS4_HUMAN | |
Accessioni | Q9NPD3Primary (citable) accession number: Q9NPD3 | |
Entry historyi | Integrated 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 statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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