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Protein

Exosome complex component MTR3

Gene

EXOSC6

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.1 Publication

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

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.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component MTR3
Alternative name(s):
Exosome component 6
mRNA transport regulator 3 homolog
Short name:
hMtr3
p11
Gene namesi
Name:EXOSC6
Synonyms:MTR3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:19055. EXOSC6.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi118460.
OpenTargetsiENSG00000223496.
PharmGKBiPA134932096.

Polymorphism and mutation databases

BioMutaiEXOSC6.
DMDMi74736141.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002874781 – 272Exosome complex component MTR3Add BLAST272

Proteomic databases

EPDiQ5RKV6.
MaxQBiQ5RKV6.
PaxDbiQ5RKV6.
PeptideAtlasiQ5RKV6.
PRIDEiQ5RKV6.
TopDownProteomicsiQ5RKV6.

PTM databases

iPTMnetiQ5RKV6.
PhosphoSitePlusiQ5RKV6.
SwissPalmiQ5RKV6.

Expressioni

Gene expression databases

BgeeiENSG00000223496.
CleanExiHS_EXOSC6.
GenevisibleiQ5RKV6. HS.

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.2 Publications

Protein-protein interaction databases

BioGridi125608. 56 interactors.
DIPiDIP-61038N.
IntActiQ5RKV6. 19 interactors.
MINTiMINT-4887413.
STRINGi9606.ENSP00000398597.

Structurei

Secondary structure

1272
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi47 – 53Combined sources7
Beta strandi57 – 59Combined sources3
Beta strandi61 – 70Combined sources10
Beta strandi95 – 102Combined sources8
Beta strandi106 – 109Combined sources4
Helixi116 – 130Combined sources15
Turni131 – 133Combined sources3
Beta strandi143 – 152Combined sources10
Helixi157 – 172Combined sources16
Beta strandi176 – 178Combined sources3
Beta strandi181 – 184Combined sources4
Turni201 – 203Combined sources3
Helixi204 – 206Combined sources3
Beta strandi208 – 216Combined sources9
Turni217 – 220Combined sources4
Beta strandi221 – 228Combined sources8
Turni234 – 237Combined sources4
Helixi238 – 267Combined sources30

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35F1-272[»]
ProteinModelPortaliQ5RKV6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5RKV6.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiKOG1068. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG057826.
InParanoidiQ5RKV6.
KOiK12587.
OMAiGRLLCDF.
OrthoDBiEOG091G0XZ0.
PhylomeDBiQ5RKV6.
TreeFamiTF323886.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5RKV6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK
60 70 80 90 100
GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAPA ALRGRLLCDF
110 120 130 140 150
RRAPFAGRRR RAPPGGCEER ELALALQEAL EPAVRLGRYP RAQLEVSALL
160 170 180 190 200
LEDGGSALAA ALTAAALALA DAGVEMYDLV VGCGLSLAPG PAPTWLLDPT
210 220 230 240 250
RLEEERAAAG LTVALMPVLN QVAGLLGSGE GGLTESWAEA VRLGLEGCQR
260 270
LYPVLQQSLV RAARRRGAAA QP
Length:272
Mass (Da):28,235
Last modified:December 21, 2004 - v1
Checksum:iF31729E0D1545F94
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC009060 Genomic DNA. No translation available.
BC052252 mRNA. Translation: AAH52252.1.
CCDSiCCDS10887.1.
RefSeqiNP_478126.1. NM_058219.2.
UniGeneiHs.660633.
Hs.744085.

Genome annotation databases

EnsembliENST00000435634; ENSP00000398597; ENSG00000223496.
GeneIDi118460.
KEGGihsa:118460.
UCSCiuc002eym.2. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC009060 Genomic DNA. No translation available.
BC052252 mRNA. Translation: AAH52252.1.
CCDSiCCDS10887.1.
RefSeqiNP_478126.1. NM_058219.2.
UniGeneiHs.660633.
Hs.744085.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35F1-272[»]
ProteinModelPortaliQ5RKV6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125608. 56 interactors.
DIPiDIP-61038N.
IntActiQ5RKV6. 19 interactors.
MINTiMINT-4887413.
STRINGi9606.ENSP00000398597.

PTM databases

iPTMnetiQ5RKV6.
PhosphoSitePlusiQ5RKV6.
SwissPalmiQ5RKV6.

Polymorphism and mutation databases

BioMutaiEXOSC6.
DMDMi74736141.

Proteomic databases

EPDiQ5RKV6.
MaxQBiQ5RKV6.
PaxDbiQ5RKV6.
PeptideAtlasiQ5RKV6.
PRIDEiQ5RKV6.
TopDownProteomicsiQ5RKV6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000435634; ENSP00000398597; ENSG00000223496.
GeneIDi118460.
KEGGihsa:118460.
UCSCiuc002eym.2. human.

Organism-specific databases

CTDi118460.
DisGeNETi118460.
GeneCardsiEXOSC6.
HGNCiHGNC:19055. EXOSC6.
MIMi606490. gene.
neXtProtiNX_Q5RKV6.
OpenTargetsiENSG00000223496.
PharmGKBiPA134932096.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1068. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG057826.
InParanoidiQ5RKV6.
KOiK12587.
OMAiGRLLCDF.
OrthoDBiEOG091G0XZ0.
PhylomeDBiQ5RKV6.
TreeFamiTF323886.

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.

Miscellaneous databases

ChiTaRSiEXOSC6. human.
EvolutionaryTraceiQ5RKV6.
GenomeRNAii118460.
PROiQ5RKV6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000223496.
CleanExiHS_EXOSC6.
GenevisibleiQ5RKV6. HS.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiEXOS6_HUMAN
AccessioniPrimary (citable) accession number: Q5RKV6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2007
Last sequence update: December 21, 2004
Last modified: November 2, 2016
This is version 115 of the entry and version 1 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 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.