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Q5RKV6

- EXOS6_HUMAN

UniProt

Q5RKV6 - EXOS6_HUMAN

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Protein

Exosome complex component MTR3

Gene

EXOSC6

Organism
Homo sapiens (Human)
Status
Reviewed - 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

  1. poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  1. DNA deamination Source: UniProtKB
  2. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
  3. gene expression Source: Reactome
  4. isotype switching Source: UniProtKB
  5. mRNA metabolic process Source: Reactome
  6. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
  7. RNA metabolic process Source: Reactome
  8. rRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_18355. ATF4 activates genes.
REACT_20619. mRNA decay by 3' to 5' exoribonuclease.
REACT_24915. Butyrate Response Factor 1 (BRF1) destabilizes mRNA.
REACT_25042. KSRP destabilizes mRNA.
REACT_25064. Tristetraprolin (TTP) destabilizes mRNA.

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
ProteomesiUP000005640: Chromosome 16

Organism-specific databases

HGNCiHGNC:19055. EXOSC6.

Subcellular locationi

Cytoplasm Curated. Nucleusnucleolus Curated. Nucleus Curated

GO - Cellular componenti

  1. cytosol Source: Reactome
  2. exosome (RNase complex) Source: UniProtKB
  3. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134932096.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 272272Exosome complex component MTR3PRO_0000287478Add
BLAST

Proteomic databases

MaxQBiQ5RKV6.
PaxDbiQ5RKV6.
PeptideAtlasiQ5RKV6.
PRIDEiQ5RKV6.

PTM databases

PhosphoSiteiQ5RKV6.

Expressioni

Gene expression databases

BgeeiQ5RKV6.
CleanExiHS_EXOSC6.
GenevestigatoriQ5RKV6.

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. 40 interactions.
DIPiDIP-61038N.
IntActiQ5RKV6. 10 interactions.
MINTiMINT-4887413.
STRINGi9606.ENSP00000398597.

Structurei

Secondary structure

1
272
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi47 – 537Combined sources
Beta strandi57 – 593Combined sources
Beta strandi61 – 7010Combined sources
Beta strandi95 – 1028Combined sources
Beta strandi106 – 1094Combined sources
Helixi116 – 13015Combined sources
Turni131 – 1333Combined sources
Beta strandi143 – 15210Combined sources
Helixi157 – 17216Combined sources
Beta strandi176 – 1783Combined sources
Beta strandi181 – 1844Combined sources
Turni201 – 2033Combined sources
Helixi204 – 2063Combined sources
Beta strandi208 – 2169Combined sources
Turni217 – 2204Combined sources
Beta strandi221 – 2288Combined sources
Turni234 – 2374Combined sources
Helixi238 – 26730Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35F1-272[»]
ProteinModelPortaliQ5RKV6.
SMRiQ5RKV6. Positions 29-260.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5RKV6.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiNOG303282.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG057826.
InParanoidiQ5RKV6.
KOiK12587.
OMAiFDRRRIN.
OrthoDBiEOG7JX35Q.
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.1. human.

Polymorphism databases

DMDMi74736141.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC009060 Genomic DNA. No translation available.
BC052252 mRNA. Translation: AAH52252.1 .
CCDSi CCDS10887.1.
RefSeqi NP_478126.1. NM_058219.2.
UniGenei Hs.660633.
Hs.744085.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2NN6 X-ray 3.35 F 1-272 [» ]
ProteinModelPortali Q5RKV6.
SMRi Q5RKV6. Positions 29-260.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 125608. 40 interactions.
DIPi DIP-61038N.
IntActi Q5RKV6. 10 interactions.
MINTi MINT-4887413.
STRINGi 9606.ENSP00000398597.

PTM databases

PhosphoSitei Q5RKV6.

Polymorphism databases

DMDMi 74736141.

Proteomic databases

MaxQBi Q5RKV6.
PaxDbi Q5RKV6.
PeptideAtlasi Q5RKV6.
PRIDEi Q5RKV6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000435634 ; ENSP00000398597 ; ENSG00000223496 .
GeneIDi 118460.
KEGGi hsa:118460.
UCSCi uc002eym.1. human.

Organism-specific databases

CTDi 118460.
GeneCardsi GC16M070284.
HGNCi HGNC:19055. EXOSC6.
MIMi 606490. gene.
neXtProti NX_Q5RKV6.
PharmGKBi PA134932096.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG303282.
GeneTreei ENSGT00550000074804.
HOGENOMi HOG000229515.
HOVERGENi HBG057826.
InParanoidi Q5RKV6.
KOi K12587.
OMAi FDRRRIN.
OrthoDBi EOG7JX35Q.
PhylomeDBi Q5RKV6.
TreeFami TF323886.

Enzyme and pathway databases

Reactomei REACT_18355. ATF4 activates genes.
REACT_20619. mRNA decay by 3' to 5' exoribonuclease.
REACT_24915. Butyrate Response Factor 1 (BRF1) destabilizes mRNA.
REACT_25042. KSRP destabilizes mRNA.
REACT_25064. Tristetraprolin (TTP) destabilizes mRNA.

Miscellaneous databases

ChiTaRSi EXOSC6. human.
EvolutionaryTracei Q5RKV6.
GenomeRNAii 118460.
NextBioi 80292.
PROi Q5RKV6.
SOURCEi Search...

Gene expression databases

Bgeei Q5RKV6.
CleanExi HS_EXOSC6.
Genevestigatori Q5RKV6.

Family and domain databases

Gene3Di 3.30.230.70. 1 hit.
InterProi IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view ]
Pfami PF01138. RNase_PH. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The sequence and analysis of duplication-rich human chromosome 16."
    Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J.
    , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
    Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Tissue: Salivary gland.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Salivary gland.
  3. "AU binding proteins recruit the exosome to degrade ARE-containing mRNAs."
    Chen C.-Y., Gherzi R., Ong S.-E., Chan E.L., Raijmakers R., Pruijn G.J.M., Stoecklin G., Moroni C., Mann M., Karin M.
    Cell 107:451-464(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE RNA EXOSOME CORE COMPLEX.
  4. "Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring."
    Raijmakers R., Vree Egberts W., van Venrooij W.J., Pruijn G.J.M.
    J. Mol. Biol. 323:653-663(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN INTERACTION.
  5. "A protein interaction framework for human mRNA degradation."
    Lehner B., Sanderson C.M.
    Genome Res. 14:1315-1323(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN INTERACTION.
  6. "Dis3-like 1: a novel exoribonuclease associated with the human exosome."
    Staals R.H., Bronkhorst A.W., Schilders G., Slomovic S., Schuster G., Heck A.J., Raijmakers R., Pruijn G.J.
    EMBO J. 29:2358-2367(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RNA EXOSOME COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates."
    Basu U., Meng F.L., Keim C., Grinstein V., Pefanis E., Eccleston J., Zhang T., Myers D., Wasserman C.R., Wesemann D.R., Januszyk K., Gregory R.I., Deng H., Lima C.D., Alt F.W.
    Cell 144:353-363(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN DEAMINATION OF TRANSCRIBED DNA SUBSTRATE.
  9. "Reconstitution, activities, and structure of the eukaryotic RNA exosome."
    Liu Q., Greimann J.C., Lima C.D.
    Cell 127:1223-1237(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.35 ANGSTROMS), LACK OF CATALYTIC ACTIVITY, RECONSTITUTION OF THE RNA EXOSOME CORE COMPLEX.
  10. Erratum
    Liu Q., Greimann J.C., Lima C.D.
    Cell 131:188-189(2007)

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 26, 2014
This is version 96 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

External Data

Dasty 3