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UniProtKB - Q06265 (EXOS9_HUMAN)

Protein

Exosome complex component RRP45

Gene

EXOSC9

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. EXOSC9 binds to ARE-containing RNAs.4 Publications

Caution

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

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: UniProtKB
  • AU-rich element binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • RNA polymerase II activating transcription factor binding Source: Ensembl
View the complete GO annotation on QuickGO ...

GO - Biological processi

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
SIGNORiQ06265

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP45
Alternative 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
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 4

Organism-specific databases

EuPathDBiHostDB:ENSG00000123737.12
HGNCiHGNC:9137 EXOSC9
MIMi606180 gene
neXtProtiNX_Q06265

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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi388 – 391PIIL → EECP: Abolishes interaction with SETX. 1 Publication4
Mutagenesisi388 – 391Missing : Abolishes interaction with SETX. 1 Publication4
Mutagenesisi390 – 391Missing : Abolishes interaction with SETX. 1 Publication2
Mutagenesisi395 – 398EEEE → AAAA: Abolishes interaction with SETX. 1 Publication4
Mutagenesisi395 – 398Missing : Abolishes interaction with SETX. 1 Publication4

Organism-specific databases

DisGeNETi5393
OpenTargetsiENSG00000123737
PharmGKBiPA33463

Polymorphism and mutation databases

BioMutaiEXOSC9
DMDMi147744559

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001399711 – 439Exosome complex component RRP45Add BLAST439

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei65PhosphoserineCombined sources1
Modified residuei297N6-acetyllysine; alternateCombined sources1
Cross-linki297Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources
Cross-linki297Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei306PhosphoserineCombined sources1
Modified residuei346PhosphoserineCombined sources1
Modified residuei392PhosphoserineCombined sources1
Modified residuei394PhosphoserineCombined sources1
Cross-linki419Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Isoform 4 (identifier: Q06265-4)
Modified residuei325PhosphoserineCombined sources1
Modified residuei327PhosphoserineCombined sources1
Isoform 2 (identifier: Q06265-2)
Modified residuei409PhosphoserineCombined sources1
Modified residuei411PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ06265
MaxQBiQ06265
PaxDbiQ06265
PeptideAtlasiQ06265
PRIDEiQ06265
ProteomicsDBi58426
58427 [Q06265-2]
58428 [Q06265-3]
58429 [Q06265-4]

PTM databases

iPTMnetiQ06265
PhosphoSitePlusiQ06265

Expressioni

Gene expression databases

BgeeiENSG00000123737 Expressed in 225 organ(s), highest expression level in female gonad
CleanExiHS_EXOSC9
ExpressionAtlasiQ06265 baseline and differential
GenevisibleiQ06265 HS

Organism-specific databases

HPAiCAB070171
HPA041838
HPA048257

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 (PubMed:11719186, PubMed:12788944, PubMed:20531389). Interacts (via C-terminus region) with SETX (via N-terminus domain); the interaction enhances SETX sumoylation (PubMed:24105744).4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EXOSC4Q9NPD35EBI-347966,EBI-371823

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGridi111402, 52 interactors
ComplexPortaliCPX-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
CORUMiQ06265
DIPiDIP-31286N
IntActiQ06265, 41 interactors
MINTiQ06265
STRINGi9606.ENSP00000368984

Structurei

Secondary structure

1439
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ06265
SMRiQ06265
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ06265

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 268ARE bindingAdd BLAST268

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiKOG1614 Eukaryota
COG2123 LUCA
GeneTreeiENSGT00530000063093
HOGENOMiHOG000229504
HOVERGENiHBG051523
InParanoidiQ06265
KOiK03678
OMAiMFMNSNL
OrthoDBiEOG091G08FZ
PhylomeDBiQ06265
TreeFamiTF300092

Family and domain databases

CDDicd11368 RNase_PH_RRP45, 1 hit
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
IPR033100 Rrp45
PfamiView protein in Pfam
PF01138 RNase_PH, 1 hit
PF03725 RNase_PH_C, 1 hit
SUPFAMiSSF54211 SSF54211, 2 hits
SSF55666 SSF55666, 1 hit

Sequences (4+)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 4 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q06265-1) [UniParc]FASTAAdd to basket
Also known as: PM/SCL-75c-alpha

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.

« Hide
        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
Length:439
Mass (Da):48,949
Last modified:May 15, 2007 - v3
Checksum:i7E27322F094ED3F3
GO
Isoform 2 (identifier: Q06265-2) [UniParc]FASTAAdd to basket
Also known as: PM/SCL-75c-beta

The sequence of this isoform differs from the canonical sequence as follows:
     385-385: Q → QELGFHHVGQTGLEFLTS

Show »
Length:456
Mass (Da):50,803
Checksum:i693B31BE41C55545
GO
Isoform 3 (identifier: Q06265-3) [UniParc]FASTAAdd to basket
Also known as: PM/SCL-75a-alpha

The sequence of this isoform differs from the canonical sequence as follows:
     1-84: Missing.

Show »
Length:355
Mass (Da):39,235
Checksum:iDC37BB31767B6621
GO
Isoform 4 (identifier: Q06265-4) [UniParc]FASTAAdd to basket
Also known as: PM/SCL-75a-beta

The sequence of this isoform differs from the canonical sequence as follows:
     1-84: Missing.
     385-385: Q → QELGFHHVGQTGLEFLTS

Show »
Length:372
Mass (Da):41,089
Checksum:iDB666F47B5422E7E
GO

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D6RIY6D6RIY6_HUMAN
Exosome complex component RRP45
EXOSC9 hCG_38830
423Annotation score:
D6RA17D6RA17_HUMAN
Exosome complex component RRP45
EXOSC9 hCG_38830
242Annotation score:
D6R905D6R905_HUMAN
Exosome complex component RRP45
EXOSC9
226Annotation score:
D6RAP4D6RAP4_HUMAN
Exosome complex component RRP45
EXOSC9
86Annotation score:
H0Y9L5H0Y9L5_HUMAN
Exosome complex component RRP45
EXOSC9
172Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_051867366I → V. Corresponds to variant dbSNP:rs1803183Ensembl.1
Natural variantiVAR_014924425S → T. Corresponds to variant dbSNP:rs1051881Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0255551 – 84Missing in isoform 3 and isoform 4. 2 PublicationsAdd BLAST84
Alternative sequenceiVSP_025556385Q → QELGFHHVGQTGLEFLTS in isoform 2 and isoform 4. 2 Publications1

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
CCDSiCCDS34057.1 [Q06265-2]
CCDS3722.2 [Q06265-1]
PIRiG01425
RefSeqiNP_001029366.1, NM_001034194.1 [Q06265-2]
NP_005024.2, NM_005033.2 [Q06265-1]
UniGeneiHs.91728

Genome annotation databases

EnsembliENST00000243498; ENSP00000243498; ENSG00000123737 [Q06265-1]
ENST00000379663; ENSP00000368984; ENSG00000123737 [Q06265-2]
GeneIDi5393
KEGGihsa:5393
UCSCiuc003idz.4 human [Q06265-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar 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
CCDSiCCDS34057.1 [Q06265-2]
CCDS3722.2 [Q06265-1]
PIRiG01425
RefSeqiNP_001029366.1, NM_001034194.1 [Q06265-2]
NP_005024.2, NM_005033.2 [Q06265-1]
UniGeneiHs.91728

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35A1-302[»]
6D6Qelectron microscopy3.45A1-439[»]
6D6Relectron microscopy3.45A1-439[»]
6H25electron microscopy3.80A1-439[»]
ProteinModelPortaliQ06265
SMRiQ06265
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111402, 52 interactors
ComplexPortaliCPX-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
CORUMiQ06265
DIPiDIP-31286N
IntActiQ06265, 41 interactors
MINTiQ06265
STRINGi9606.ENSP00000368984

PTM databases

iPTMnetiQ06265
PhosphoSitePlusiQ06265

Polymorphism and mutation databases

BioMutaiEXOSC9
DMDMi147744559

Proteomic databases

EPDiQ06265
MaxQBiQ06265
PaxDbiQ06265
PeptideAtlasiQ06265
PRIDEiQ06265
ProteomicsDBi58426
58427 [Q06265-2]
58428 [Q06265-3]
58429 [Q06265-4]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000243498; ENSP00000243498; ENSG00000123737 [Q06265-1]
ENST00000379663; ENSP00000368984; ENSG00000123737 [Q06265-2]
GeneIDi5393
KEGGihsa:5393
UCSCiuc003idz.4 human [Q06265-1]

Organism-specific databases

CTDi5393
DisGeNETi5393
EuPathDBiHostDB:ENSG00000123737.12
GeneCardsiEXOSC9
HGNCiHGNC:9137 EXOSC9
HPAiCAB070171
HPA041838
HPA048257
MIMi606180 gene
neXtProtiNX_Q06265
OpenTargetsiENSG00000123737
PharmGKBiPA33463
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1614 Eukaryota
COG2123 LUCA
GeneTreeiENSGT00530000063093
HOGENOMiHOG000229504
HOVERGENiHBG051523
InParanoidiQ06265
KOiK03678
OMAiMFMNSNL
OrthoDBiEOG091G08FZ
PhylomeDBiQ06265
TreeFamiTF300092

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
SIGNORiQ06265

Miscellaneous databases

ChiTaRSiEXOSC9 human
EvolutionaryTraceiQ06265
GeneWikiiExosome_component_9
GenomeRNAii5393
PROiPR:Q06265
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000123737 Expressed in 225 organ(s), highest expression level in female gonad
CleanExiHS_EXOSC9
ExpressionAtlasiQ06265 baseline and differential
GenevisibleiQ06265 HS

Family and domain databases

CDDicd11368 RNase_PH_RRP45, 1 hit
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
IPR033100 Rrp45
PfamiView protein in Pfam
PF01138 RNase_PH, 1 hit
PF03725 RNase_PH_C, 1 hit
SUPFAMiSSF54211 SSF54211, 2 hits
SSF55666 SSF55666, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiEXOS9_HUMAN
AccessioniPrimary (citable) accession number: Q06265
Secondary accession number(s): Q12883
, Q4W5P5, Q86Y41, Q86Y48
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: May 15, 2007
Last modified: October 10, 2018
This is version 179 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. SIMILARITY comments
    Index of protein domains and families
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  6. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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