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Q5RKV6

- EXOS6_HUMAN

UniProt

Q5RKV6 - EXOS6_HUMAN

Protein

Exosome complex component MTR3

Gene

EXOSC6

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      Previous versions | rss
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    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

    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. nucleolus Source: UniProtKB-SubCell

    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. 39 interactions.
    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 – 537
    Beta strandi57 – 593
    Beta strandi61 – 7010
    Beta strandi95 – 1028
    Beta strandi106 – 1094
    Helixi116 – 13015
    Turni131 – 1333
    Beta strandi143 – 15210
    Helixi157 – 17216
    Beta strandi176 – 1783
    Beta strandi181 – 1844
    Turni201 – 2033
    Helixi204 – 2063
    Beta strandi208 – 2169
    Turni217 – 2204
    Beta strandi221 – 2288
    Turni234 – 2374
    Helixi238 – 26730

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    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

    MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK    50
    GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAPA ALRGRLLCDF 100
    RRAPFAGRRR RAPPGGCEER ELALALQEAL EPAVRLGRYP RAQLEVSALL 150
    LEDGGSALAA ALTAAALALA DAGVEMYDLV VGCGLSLAPG PAPTWLLDPT 200
    RLEEERAAAG LTVALMPVLN QVAGLLGSGE GGLTESWAEA VRLGLEGCQR 250
    LYPVLQQSLV RAARRRGAAA QP 272
    Length:272
    Mass (Da):28,235
    Last modified:December 21, 2004 - v1
    Checksum:iF31729E0D1545F94
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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. 39 interactions.
    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.
    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

    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: October 1, 2014
    This is version 94 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