Q9NQT5 · EXOS3_HUMAN
- ProteinExosome complex component RRP40
- GeneEXOSC3
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids275 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
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.
GO annotations
all annotations | all molecular function | virus receptor activity | dna binding | rna binding | cytoskeletal motor activity | catalytic activity | gtpase activity | structural molecule activity | transporter activity | cytoskeletal protein binding | lipid binding | cyclase activity | antioxidant activity | oxidoreductase activity | transferase activity | hydrolase activity | lyase activity | isomerase activity | ligase activity | protein tag activity | cargo receptor activity | histone binding | protein folding chaperone | translation regulator activity | nutrient reservoir activity | receptor ligand activity | molecular transducer activity | molecular adaptor activity | toxin activity | cell adhesion mediator activity | molecular function regulator activity | virus coreceptor activity | catalytic activity, acting on a protein | catalytic activity, acting on dna | catalytic activity, acting on rna | molecular carrier activity | transcription regulator activity | general transcription initiation factor activity | molecular sensor activity | molecular sequestering activity | atp-dependent activity | other molecular function | all biological process | mitotic cell cycle | cytokinesis | cytoplasmic translation | immune system process | muscle system process | circulatory system process | renal system process | respiratory system process | carbohydrate metabolic process | generation of precursor metabolites and energy | dna replication | dna repair | dna recombination | chromatin organization | dna-templated transcription | regulation of dna-templated transcription | trna metabolic process | protein folding | protein glycosylation | amino acid metabolic process | modified amino acid metabolic process | lipid metabolic process | vitamin metabolic process | sulfur compound metabolic process | intracellular protein transport | nucleocytoplasmic transport | autophagy | inflammatory response | mitochondrion organization | cytoskeleton organization | microtubule-based movement | peroxisome organization | lysosome organization | chromosome segregation | cell adhesion | establishment or maintenance of cell polarity | programmed cell death | photosynthesis | mrna metabolic process | snrna metabolic process | vesicle-mediated transport | reproductive process | digestive system process | signaling | cell differentiation | protein catabolic process | extracellular matrix organization | regulatory ncrna-mediated gene silencing | telomere organization | cell junction organization | wound healing | ribosome biogenesis | cilium organization | anatomical structure development | cell motility | nervous system process | endocrine process | protein maturation | transmembrane transport | nucleobase-containing small molecule metabolic process | hepaticobiliary system process | membrane organization | protein-containing complex assembly | cell wall organization or biogenesis | nitrogen cycle metabolic process | protein localization to plasma membrane | defense response to other organism | detoxification | meiotic nuclear division | mitotic nuclear division | mitochondrial gene expression | carbohydrate derivative metabolic process | other biological process | all cellular component | nuclear chromosome | extracellular region | extracellular space | cell wall | nucleus | nuclear envelope | nucleoplasm | chromosome | nucleolus | mitochondrion | lysosome | endosome | vacuole | peroxisome | endoplasmic reticulum | golgi apparatus | lipid droplet | microtubule organizing center | cytosol | ribosome | cytoskeleton | plasma membrane | cilium | plastid | thylakoid | external encapsulating structure | extracellular matrix | cytoplasmic vesicle | organelle | other cellular component | |||
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Keywords
- Molecular function
- Biological process
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameExosome complex component RRP40
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionQ9NQT5
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Disease & Variants
Involvement in disease
Pontocerebellar hypoplasia 1B (PCH1B)
- Note
- 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 alsoMIM:614678
Natural variants in PCH1B
Variant ID | Position(s) | Change | Description | |
---|---|---|---|---|
VAR_068505 | 31 | G>A | in PCH1B; dbSNP:rs387907196 | |
VAR_068506 | 132 | D>A | in PCH1B; dbSNP:rs141138948 | |
VAR_068507 | 139 | A>P | in PCH1B; dbSNP:rs387907195 | |
VAR_068508 | 238 | W>R | in PCH1B; dbSNP:rs672601332 |
Features
Showing features for natural variant.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Natural variant | VAR_068505 | 31 | in PCH1B; dbSNP:rs387907196 | |||
Sequence: G → A | ||||||
Natural variant | VAR_074169 | 80 | in dbSNP:rs374550999 | |||
Sequence: V → F | ||||||
Natural variant | VAR_068506 | 132 | in PCH1B; dbSNP:rs141138948 | |||
Sequence: D → A | ||||||
Natural variant | VAR_068507 | 139 | in PCH1B; dbSNP:rs387907195 | |||
Sequence: A → P | ||||||
Natural variant | VAR_054098 | 225 | in dbSNP:rs3208406 | |||
Sequence: Y → H | ||||||
Natural variant | VAR_068508 | 238 | in PCH1B; dbSNP:rs672601332 | |||
Sequence: W → R |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 374 variants from UniProt as well as other sources including ClinVar and dbSNP.
Keywords
- Disease
Organism-specific databases
Miscellaneous
Genetic variation databases
PTM/Processing
Features
Showing features for initiator methionine, modified residue, chain, modified residue (large scale data), cross-link.
Type | ID | Position(s) | Source | Description | |||
---|---|---|---|---|---|---|---|
Initiator methionine | 1 | UniProt | Removed | ||||
Sequence: M | |||||||
Modified residue | 2 | UniProt | N-acetylalanine | ||||
Sequence: A | |||||||
Chain | PRO_0000087131 | 2-275 | UniProt | Exosome complex component RRP40 | |||
Sequence: AEPASVAAESLAGSRARAARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAES | |||||||
Modified residue (large scale data) | 6 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 11 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Cross-link | 151 | UniProt | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K |
Keywords
- PTM
Proteomic databases
PTM databases
Interaction
Subunit
Component of the RNA exosome complex (PubMed:29906447).
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. Interacts with DHX36; this interaction occurs in a RNase-insensitive manner (PubMed:14731398).
Interacts with HBS1L isoform 2 (PubMed:28204585).
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. Interacts with DHX36; this interaction occurs in a RNase-insensitive manner (PubMed:14731398).
Interacts with HBS1L isoform 2 (PubMed:28204585).
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | Q9NQT5 | DDX17 Q92841 | 2 | EBI-371866, EBI-746012 | |
BINARY | Q9NQT5 | DIS3 Q9Y2L1 | 4 | EBI-371866, EBI-373539 | |
BINARY | Q9NQT5 | DIS3L Q8TF46 | 7 | EBI-371866, EBI-3672244 | |
BINARY | Q9NQT5 | EXOSC2 Q13868 | 10 | EBI-371866, EBI-301735 | |
BINARY | Q9NQT5 | EXOSC4 Q9NPD3 | 9 | EBI-371866, EBI-371823 | |
BINARY | Q9NQT5 | EXOSC5 Q9NQT4 | 12 | EBI-371866, EBI-371876 | |
BINARY | Q9NQT5 | EXOSC8 Q96B26 | 7 | EBI-371866, EBI-371922 | |
BINARY | Q9NQT5 | TSR2 Q969E8 | 3 | EBI-371866, EBI-746981 | |
XENO | Q9NQT5 | Zc3hav1 Q8K3Y6 | 3 | EBI-371866, EBI-8860250 |
Protein-protein interaction databases
Miscellaneous
Structure
Sequence & Isoform
- Sequence statusComplete
This entry describes 2 isoforms produced by Alternative splicing.
Q9NQT5-1
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.
- Name1
- Length275
- Mass (Da)29,572
- Last updated2007-01-23 v3
- Checksum264322144A199166
Q9NQT5-2
- Name2
- Differences from canonical
- 159-275: VGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAES → AISSRL
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
A0A7I2V328 | A0A7I2V328_HUMAN | EXOSC3 | 93 |
Features
Showing features for sequence conflict, alternative sequence.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 56-65 | in Ref. 7; AAD34097 | ||||
Sequence: NARACSRVRV → MLERARGCAF | ||||||
Sequence conflict | 95 | in Ref. 7; AAD34097 | ||||
Sequence: S → G | ||||||
Alternative sequence | VSP_043457 | 159-275 | in isoform 2 | |||
Sequence: VGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAES → AISSRL |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AF281132 EMBL· GenBank· DDBJ | AAF82133.1 EMBL· GenBank· DDBJ | mRNA | ||
AK289571 EMBL· GenBank· DDBJ | BAF82260.1 EMBL· GenBank· DDBJ | mRNA | ||
AK290864 EMBL· GenBank· DDBJ | BAF83553.1 EMBL· GenBank· DDBJ | mRNA | ||
AL138752 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
CH471071 EMBL· GenBank· DDBJ | EAW58264.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BC002437 EMBL· GenBank· DDBJ | AAH02437.1 EMBL· GenBank· DDBJ | mRNA | ||
BC008880 EMBL· GenBank· DDBJ | AAH08880.1 EMBL· GenBank· DDBJ | mRNA | ||
AF151860 EMBL· GenBank· DDBJ | AAD34097.1 EMBL· GenBank· DDBJ | mRNA |