UniProtKB - Q06265 (EXOS9_HUMAN)
Exosome complex component RRP45
EXOSC9
Functioni
Caution
GO - Molecular functioni
- 3'-5'-exoribonuclease activity Source: UniProtKB
- mRNA 3'-UTR AU-rich region binding Source: GO_Central
- RNA binding Source: UniProtKB
- RNA polymerase II activating transcription factor binding Source: Ensembl
GO - Biological processi
- exonucleolytic catabolism of deadenylated mRNA Source: UniProtKB
- exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: GO_Central
- immune response Source: UniProtKB
- nuclear mRNA surveillance Source: UniProtKB
- nuclear polyadenylation-dependent mRNA catabolic process Source: GO_Central
- nuclear polyadenylation-dependent rRNA catabolic process Source: UniProtKB
- nuclear polyadenylation-dependent tRNA catabolic process Source: GO_Central
- nuclear-transcribed mRNA catabolic process Source: UniProtKB
- nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: GO_Central
- positive regulation of cell growth Source: UniProtKB
- positive regulation of transcription by RNA polymerase II Source: Ensembl
- regulation of mRNA stability Source: Reactome
- rRNA catabolic process Source: GO_Central
- rRNA processing Source: Reactome
- U1 snRNA 3'-end processing Source: GO_Central
- U4 snRNA 3'-end processing Source: GO_Central
- U5 snRNA 3'-end processing Source: GO_Central
Keywordsi
Molecular function | RNA-binding |
Biological process | rRNA processing |
Enzyme and pathway databases
PathwayCommonsi | Q06265 |
Reactomei | R-HSA-380994, ATF4 activates genes in response to endoplasmic reticulum stress 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 |
SIGNORi | Q06265 |
Names & Taxonomyi
Protein namesi | Recommended name: Exosome complex component RRP45Alternative name(s): Autoantigen PM/Scl 1 Exosome component 9 P75 polymyositis-scleroderma overlap syndrome-associated autoantigen Polymyositis/scleroderma autoantigen 1 Polymyositis/scleroderma autoantigen 75 kDa Short name: PM/Scl-75 |
Gene namesi | Name:EXOSC9 Synonyms:PMSCL1 |
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
HGNCi | HGNC:9137, EXOSC9 |
MIMi | 606180, gene |
neXtProti | NX_Q06265 |
VEuPathDBi | HostDB:ENSG00000123737.12 |
Subcellular locationi
Nucleus
- Nucleus 1 Publication
- nucleolus 1 Publication
- nucleoplasm 1 Publication
Cytoplasm and Cytosol
- Cytoplasm 1 Publication
Note: Colocalizes with SETX in nuclear foci upon induction of transcription-related DNA damage at the S phase (PubMed:24105744).1 Publication
Nucleus
Nucleus
Nucleus
Note: Excluded from the nucleolus.
Cytosol
- cytosol Source: Reactome
Extracellular region or secreted
- extracellular exosome Source: UniProtKB
Nucleus
- nuclear chromosome Source: UniProtKB
- nuclear exosome (RNase complex) Source: UniProtKB
- nucleolus Source: UniProtKB
- nucleoplasm Source: UniProtKB
- nucleus Source: UniProtKB
Other locations
- cytoplasm Source: UniProtKB
- cytoplasmic exosome (RNase complex) Source: GO_Central
- exosome (RNase complex) Source: UniProtKB
Keywords - Cellular componenti
Cytoplasm, Exosome, NucleusPathology & Biotechi
Involvement in diseasei
Pontocerebellar hypoplasia 1D (PCH1D)1 Publication
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_081052 | 14 | L → P in PCH1D; reduced EXOSC9 and exosome levels in patient cells. 1 PublicationCorresponds to variant dbSNP:rs139632595EnsemblClinVar. | 1 | |
Natural variantiVAR_081053 | 161 – 439 | Missing in PCH1D; reduced EXOSC9 and exosome levels in patient cells. 1 PublicationAdd BLAST | 279 |
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 388 – 391 | PIIL → EECP: Abolishes interaction with SETX. 1 Publication | 4 | |
Mutagenesisi | 388 – 391 | Missing : Abolishes interaction with SETX. 1 Publication | 4 | |
Mutagenesisi | 390 – 391 | Missing : Abolishes interaction with SETX. 1 Publication | 2 | |
Mutagenesisi | 395 – 398 | EEEE → AAAA: Abolishes interaction with SETX. 1 Publication | 4 | |
Mutagenesisi | 395 – 398 | Missing : Abolishes interaction with SETX. 1 Publication | 4 |
Keywords - Diseasei
Disease variant, NeurodegenerationOrganism-specific databases
DisGeNETi | 5393 |
MalaCardsi | EXOSC9 |
MIMi | 618065, phenotype |
OpenTargetsi | ENSG00000123737 |
Orphaneti | 2254, Pontocerebellar hypoplasia type 1 |
PharmGKBi | PA33463 |
Miscellaneous databases
Pharosi | Q06265, Tbio |
Genetic variation databases
BioMutai | EXOSC9 |
DMDMi | 147744559 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000139971 | 1 – 439 | Exosome complex component RRP45Add BLAST | 439 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length | |
---|---|---|---|---|---|
Modified residuei | 65 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 297 | N6-acetyllysine; alternateCombined sources | 1 | ||
Cross-linki | 297 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources | |||
Cross-linki | 297 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources | |||
Modified residuei | 306 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 346 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 392 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 394 | PhosphoserineCombined sources | 1 | ||
Cross-linki | 419 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | |||
Isoform 4 (identifier: Q06265-4) | |||||
Modified residuei | 325 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 327 | PhosphoserineCombined sources | 1 | ||
Isoform 2 (identifier: Q06265-2) | |||||
Modified residuei | 409 | PhosphoserineCombined sources | 1 | ||
Modified residuei | 411 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | Q06265 |
jPOSTi | Q06265 |
MassIVEi | Q06265 |
MaxQBi | Q06265 |
PaxDbi | Q06265 |
PeptideAtlasi | Q06265 |
PRIDEi | Q06265 |
ProteomicsDBi | 58426 [Q06265-1] 58427 [Q06265-2] 58428 [Q06265-3] 58429 [Q06265-4] |
PTM databases
iPTMneti | Q06265 |
PhosphoSitePlusi | Q06265 |
SwissPalmi | Q06265 |
Expressioni
Gene expression databases
Bgeei | ENSG00000123737, Expressed in female gonad and 234 other tissues |
ExpressionAtlasi | Q06265, baseline and differential |
Genevisiblei | Q06265, HS |
Organism-specific databases
HPAi | ENSG00000123737, Low tissue specificity |
Interactioni
Subunit structurei
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 (PubMed:11719186, PubMed:12788944, PubMed:20531389).
Interacts (via C-terminus region) with SETX (via N-terminus domain); the interaction enhances SETX sumoylation (PubMed:24105744).
5 PublicationsBinary interactionsi
Q06265
With | #Exp. | IntAct |
---|---|---|
EXOSC4 [Q9NPD3] | 7 | EBI-347966,EBI-371823 |
GO - Molecular functioni
- RNA polymerase II activating transcription factor binding Source: Ensembl
Protein-protein interaction databases
BioGRIDi | 111402, 94 interactors |
ComplexPortali | CPX-476, Nuclear exosome complex, DIS3-EXOSC10 variant CPX-591, Nucleolar exosome complex, EXOSC10 variant CPX-592, Cytoplasmic exosome complex, DIS3L variant CPX-593, Exosome complex, DIS3 variant CPX-600, Cytoplasmic exosome complex, DIS3L-EXOSC10 variant |
CORUMi | Q06265 |
DIPi | DIP-31286N |
IntActi | Q06265, 51 interactors |
MINTi | Q06265 |
STRINGi | 9606.ENSP00000368984 |
Miscellaneous databases
RNActi | Q06265, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q06265 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q06265 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 1 – 268 | ARE binding1 PublicationAdd BLAST | 268 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG1614, Eukaryota |
GeneTreei | ENSGT00950000183130 |
HOGENOMi | CLU_038194_7_0_1 |
InParanoidi | Q06265 |
OMAi | HGEICQI |
OrthoDBi | 996662at2759 |
PhylomeDBi | Q06265 |
TreeFami | TF300092 |
Family and domain databases
CDDi | cd11368, RNase_PH_RRP45, 1 hit |
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 IPR033100, Rrp45 |
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 |
s (4+)i Sequence
Sequence statusi: Complete.
This entry describes 4 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 4 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MKETPLSNCE RRFLLRAIEE KKRLDGRQTY DYRNIRISFG TDYGCCIVEL
60 70 80 90 100
GKTRVLGQVS CELVSPKLNR ATEGILFFNL ELSQMAAPAF EPGRQSDLLV
110 120 130 140 150
KLNRLMERCL RNSKCIDTES LCVVAGEKVW QIRVDLHLLN HDGNIIDAAS
160 170 180 190 200
IAAIVALCHF RRPDVSVQGD EVTLYTPEER DPVPLSIHHM PICVSFAFFQ
210 220 230 240 250
QGTYLLVDPN EREERVMDGL LVIAMNKHRE ICTIQSSGGI MLLKDQVLRC
260 270 280 290 300
SKIAGVKVAE ITELILKALE NDQKVRKEGG KFGFAESIAN QRITAFKMEK
310 320 330 340 350
APIDTSDVEE KAEEIIAEAE PPSEVVSTPV LWTPGTAQIG EGVENSWGDL
360 370 380 390 400
EDSEKEDDEG GGDQAIILDG IKMDTGVEVS DIGSQDAPII LSDSEEEEMI
410 420 430
ILEPDKNPKK IRTQTTSAKQ EKAPSKKPVK RRKKKRAAN
Computationally mapped potential isoform sequencesi
There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketD6RIY6 | D6RIY6_HUMAN | Exosome complex component RRP45 | EXOSC9 hCG_38830 | 423 | Annotation score: | ||
D6R905 | D6R905_HUMAN | Exosome complex component RRP45 | EXOSC9 | 226 | Annotation score: | ||
D6RA17 | D6RA17_HUMAN | Exosome complex component RRP45 | EXOSC9 hCG_38830 | 242 | Annotation score: | ||
H0Y9L5 | H0Y9L5_HUMAN | Exosome complex component RRP45 | EXOSC9 | 172 | Annotation score: | ||
D6RAP4 | D6RAP4_HUMAN | Exosome complex component RRP45 | EXOSC9 | 86 | Annotation score: |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_081052 | 14 | L → P in PCH1D; reduced EXOSC9 and exosome levels in patient cells. 1 PublicationCorresponds to variant dbSNP:rs139632595EnsemblClinVar. | 1 | |
Natural variantiVAR_081053 | 161 – 439 | Missing in PCH1D; reduced EXOSC9 and exosome levels in patient cells. 1 PublicationAdd BLAST | 279 | |
Natural variantiVAR_051867 | 366 | I → V. Corresponds to variant dbSNP:rs1803183Ensembl. | 1 | |
Natural variantiVAR_014924 | 425 | S → T. Corresponds to variant dbSNP:rs1051881Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_025555 | 1 – 84 | Missing in isoform 3 and isoform 4. 2 PublicationsAdd BLAST | 84 | |
Alternative sequenceiVSP_025556 | 385 | Q → QELGFHHVGQTGLEFLTS in isoform 2 and isoform 4. 2 Publications | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M58460 mRNA Translation: AAA58384.1 U09215 mRNA Translation: AAA18832.1 AJ505989 mRNA Translation: CAD44530.1 AJ517294 mRNA Translation: CAD56889.1 AC079341 Genomic DNA Translation: AAY40968.1 |
CCDSi | CCDS34057.1 [Q06265-2] CCDS3722.2 [Q06265-1] |
PIRi | G01425 |
RefSeqi | NP_001029366.1, NM_001034194.1 [Q06265-2] NP_005024.2, NM_005033.2 [Q06265-1] |
Genome annotation databases
Ensembli | ENST00000243498; ENSP00000243498; ENSG00000123737 [Q06265-1] ENST00000379663; ENSP00000368984; ENSG00000123737 [Q06265-2] |
GeneIDi | 5393 |
KEGGi | hsa:5393 |
UCSCi | uc003idz.4, human [Q06265-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M58460 mRNA Translation: AAA58384.1 U09215 mRNA Translation: AAA18832.1 AJ505989 mRNA Translation: CAD44530.1 AJ517294 mRNA Translation: CAD56889.1 AC079341 Genomic DNA Translation: AAY40968.1 |
CCDSi | CCDS34057.1 [Q06265-2] CCDS3722.2 [Q06265-1] |
PIRi | G01425 |
RefSeqi | NP_001029366.1, NM_001034194.1 [Q06265-2] NP_005024.2, NM_005033.2 [Q06265-1] |
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 | A | 1-302 | [»] | |
6D6Q | electron microscopy | 3.45 | A | 1-439 | [»] | |
6D6R | electron microscopy | 3.45 | A | 1-439 | [»] | |
6H25 | electron microscopy | 3.80 | A | 1-439 | [»] | |
SMRi | Q06265 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 111402, 94 interactors |
ComplexPortali | CPX-476, Nuclear exosome complex, DIS3-EXOSC10 variant CPX-591, Nucleolar exosome complex, EXOSC10 variant CPX-592, Cytoplasmic exosome complex, DIS3L variant CPX-593, Exosome complex, DIS3 variant CPX-600, Cytoplasmic exosome complex, DIS3L-EXOSC10 variant |
CORUMi | Q06265 |
DIPi | DIP-31286N |
IntActi | Q06265, 51 interactors |
MINTi | Q06265 |
STRINGi | 9606.ENSP00000368984 |
PTM databases
iPTMneti | Q06265 |
PhosphoSitePlusi | Q06265 |
SwissPalmi | Q06265 |
Genetic variation databases
BioMutai | EXOSC9 |
DMDMi | 147744559 |
Proteomic databases
EPDi | Q06265 |
jPOSTi | Q06265 |
MassIVEi | Q06265 |
MaxQBi | Q06265 |
PaxDbi | Q06265 |
PeptideAtlasi | Q06265 |
PRIDEi | Q06265 |
ProteomicsDBi | 58426 [Q06265-1] 58427 [Q06265-2] 58428 [Q06265-3] 58429 [Q06265-4] |
Protocols and materials databases
Antibodypediai | 26749, 144 antibodies |
Genome annotation databases
Ensembli | ENST00000243498; ENSP00000243498; ENSG00000123737 [Q06265-1] ENST00000379663; ENSP00000368984; ENSG00000123737 [Q06265-2] |
GeneIDi | 5393 |
KEGGi | hsa:5393 |
UCSCi | uc003idz.4, human [Q06265-1] |
Organism-specific databases
CTDi | 5393 |
DisGeNETi | 5393 |
GeneCardsi | EXOSC9 |
HGNCi | HGNC:9137, EXOSC9 |
HPAi | ENSG00000123737, Low tissue specificity |
MalaCardsi | EXOSC9 |
MIMi | 606180, gene 618065, phenotype |
neXtProti | NX_Q06265 |
OpenTargetsi | ENSG00000123737 |
Orphaneti | 2254, Pontocerebellar hypoplasia type 1 |
PharmGKBi | PA33463 |
VEuPathDBi | HostDB:ENSG00000123737.12 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG1614, Eukaryota |
GeneTreei | ENSGT00950000183130 |
HOGENOMi | CLU_038194_7_0_1 |
InParanoidi | Q06265 |
OMAi | HGEICQI |
OrthoDBi | 996662at2759 |
PhylomeDBi | Q06265 |
TreeFami | TF300092 |
Enzyme and pathway databases
PathwayCommonsi | Q06265 |
Reactomei | R-HSA-380994, ATF4 activates genes in response to endoplasmic reticulum stress 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 |
SIGNORi | Q06265 |
Miscellaneous databases
BioGRID-ORCSi | 5393, 645 hits in 1007 CRISPR screens |
ChiTaRSi | EXOSC9, human |
EvolutionaryTracei | Q06265 |
GeneWikii | Exosome_component_9 |
GenomeRNAii | 5393 |
Pharosi | Q06265, Tbio |
PROi | PR:Q06265 |
RNActi | Q06265, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000123737, Expressed in female gonad and 234 other tissues |
ExpressionAtlasi | Q06265, baseline and differential |
Genevisiblei | Q06265, HS |
Family and domain databases
CDDi | cd11368, RNase_PH_RRP45, 1 hit |
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 IPR033100, Rrp45 |
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 |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | EXOS9_HUMAN | |
Accessioni | Q06265Primary (citable) accession number: Q06265 Secondary accession number(s): Q12883 Q86Y48 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 1, 2001 |
Last sequence update: | May 15, 2007 | |
Last modified: | April 7, 2021 | |
This is version 199 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
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Human chromosome 4
Human chromosome 4: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families