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Protein

Exosome complex component RRP45

Gene

EXOSC9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: UniProtKB
  • AU-rich element binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000123737-MONOMER.
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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:9137. EXOSC9.

Subcellular locationi

  • Cytoplasm
  • Nucleus 1 Publication
  • Nucleusnucleolus 1 Publication
  • Nucleusnucleoplasm 1 Publication

  • Note: Colocalizes with SETX in nuclear foci upon induction of transcription-related DNA damage at the S phase (PubMed:24105744).1 Publication
Isoform 3 :
  • Nucleus

  • Note: Excluded from the nucleolus.

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytoplasmic exosome (RNase complex) Source: GO_Central
  • cytosol Source: Reactome
  • exosome (RNase complex) Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • nuclear chromosome Source: UniProtKB
  • nuclear exosome (RNase complex) Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

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.

PTM databases

iPTMnetiQ06265.
PhosphoSitePlusiQ06265.

Expressioni

Gene expression databases

BgeeiENSG00000123737.
CleanExiHS_EXOSC9.
ExpressionAtlasiQ06265. baseline and differential.
GenevisibleiQ06265. HS.

Organism-specific databases

HPAiHPA041838.

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

Protein-protein interaction databases

BioGridi111402. 46 interactors.
DIPiDIP-31286N.
IntActiQ06265. 39 interactors.
MINTiMINT-1036055.
STRINGi9606.ENSP00000368984.

Structurei

Secondary structure

1439
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 19Combined sources12
Beta strandi36 – 39Combined sources4
Beta strandi45 – 52Combined sources8
Beta strandi54 – 59Combined sources6
Beta strandi62 – 64Combined sources3
Turni69 – 72Combined sources4
Beta strandi76 – 82Combined sources7
Turni84 – 86Combined sources3
Beta strandi92 – 94Combined sources3
Helixi96 – 99Combined sources4
Helixi101 – 113Combined sources13
Beta strandi118 – 121Combined sources4
Turni125 – 127Combined sources3
Beta strandi128 – 138Combined sources11
Helixi146 – 159Combined sources14
Helixi176 – 179Combined sources4
Beta strandi191 – 198Combined sources8
Turni200 – 202Combined sources3
Beta strandi203 – 208Combined sources6
Helixi211 – 216Combined sources6
Beta strandi220 – 226Combined sources7
Turni227 – 229Combined sources3
Beta strandi230 – 238Combined sources9
Helixi244 – 277Combined sources34
Helixi287 – 290Combined sources4
Beta strandi291 – 298Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35A1-302[»]
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.
OMAiKMDTGVE.
OrthoDBiEOG091G08FZ.
PhylomeDBiQ06265.
TreeFamiTF300092.

Family and domain databases

CDDicd11368. RNase_PH_RRP45. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR033100. Rrp45.
[Graphical view]
PANTHERiPTHR11097:SF14. PTHR11097:SF14. 1 hit.
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
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

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_051867366I → V.Corresponds to variant rs1803183dbSNPEnsembl.1
Natural variantiVAR_014924425S → T.Corresponds to variant rs1051881dbSNPEnsembl.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

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[»]
ProteinModelPortaliQ06265.
SMRiQ06265.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111402. 46 interactors.
DIPiDIP-31286N.
IntActiQ06265. 39 interactors.
MINTiMINT-1036055.
STRINGi9606.ENSP00000368984.

PTM databases

iPTMnetiQ06265.
PhosphoSitePlusiQ06265.

Polymorphism and mutation databases

BioMutaiEXOSC9.
DMDMi147744559.

Proteomic databases

EPDiQ06265.
MaxQBiQ06265.
PaxDbiQ06265.
PeptideAtlasiQ06265.
PRIDEiQ06265.

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.
GeneCardsiEXOSC9.
HGNCiHGNC:9137. EXOSC9.
HPAiHPA041838.
MIMi606180. gene.
neXtProtiNX_Q06265.
OpenTargetsiENSG00000123737.
PharmGKBiPA33463.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciZFISH:ENSG00000123737-MONOMER.
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

EvolutionaryTraceiQ06265.
GeneWikiiExosome_component_9.
GenomeRNAii5393.
PROiQ06265.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000123737.
CleanExiHS_EXOSC9.
ExpressionAtlasiQ06265. baseline and differential.
GenevisibleiQ06265. HS.

Family and domain databases

CDDicd11368. RNase_PH_RRP45. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR033100. Rrp45.
[Graphical view]
PANTHERiPTHR11097:SF14. PTHR11097:SF14. 1 hit.
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
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 historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: May 15, 2007
Last modified: November 2, 2016
This is version 161 of the entry and version 3 of the sequence. [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, 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. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.