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Q15024

- EXOS7_HUMAN

UniProt

Q15024 - EXOS7_HUMAN

Protein

Exosome complex component RRP42

Gene

EXOSC7

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 139 (01 Oct 2014)
      Sequence version 3 (08 Feb 2011)
      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.

    GO - Molecular functioni

    1. 3'-5'-exoribonuclease activity Source: UniProtKB
    2. protein binding Source: UniProtKB
    3. RNA binding Source: UniProtKB

    GO - Biological processi

    1. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
    2. gene expression Source: Reactome
    3. mRNA metabolic process Source: Reactome
    4. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
    5. RNA catabolic process Source: UniProtKB
    6. RNA metabolic process Source: Reactome
    7. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
    8. rRNA processing Source: UniProtKB

    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 RRP42
    Alternative name(s):
    Exosome component 7
    Ribosomal RNA-processing protein 42
    p8
    Gene namesi
    Name:EXOSC7
    Synonyms:KIAA0116, RRP42
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 3

    Organism-specific databases

    HGNCiHGNC:28112. EXOSC7.

    Subcellular locationi

    Nucleusnucleolus 1 Publication. Cytoplasm 1 Publication. Nucleus 1 Publication

    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

    PharmGKBiPA134880567.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed3 Publications
    Chaini2 – 291290Exosome complex component RRP42PRO_0000139963Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine3 Publications
    Modified residuei116 – 1161N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiQ15024.
    PaxDbiQ15024.
    PeptideAtlasiQ15024.
    PRIDEiQ15024.

    2D gel databases

    SWISS-2DPAGEQ15024.

    PTM databases

    PhosphoSiteiQ15024.

    Expressioni

    Gene expression databases

    ArrayExpressiQ15024.
    BgeeiQ15024.
    GenevestigatoriQ15024.

    Organism-specific databases

    HPAiHPA036182.

    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. Interacts with EXOSC1. Interacts with ZC3HAV1.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    EXOSC1Q9Y3B26EBI-371841,EBI-371892
    EXOSC2Q138685EBI-371841,EBI-301735

    Protein-protein interaction databases

    BioGridi116658. 18 interactions.
    DIPiDIP-31266N.
    IntActiQ15024. 16 interactions.
    MINTiMINT-1457458.
    STRINGi9606.ENSP00000265564.

    Structurei

    Secondary structure

    1
    291
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi8 – 1912
    Beta strandi24 – 263
    Beta strandi36 – 394
    Beta strandi45 – 539
    Beta strandi56 – 616
    Beta strandi71 – 733
    Beta strandi79 – 824
    Turni87 – 893
    Helixi99 – 11517
    Beta strandi121 – 1244
    Turni128 – 1303
    Beta strandi135 – 1417
    Helixi148 – 15811
    Turni159 – 1624
    Beta strandi167 – 1715
    Beta strandi180 – 1867
    Beta strandi201 – 21313
    Helixi216 – 2194
    Beta strandi223 – 2286
    Beta strandi232 – 2343
    Beta strandi238 – 2458
    Helixi249 – 27830

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2NN6X-ray3.35E1-291[»]
    ProteinModelPortaliQ15024.
    SMRiQ15024. Positions 5-285.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ15024.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RNase PH family.Curated

    Phylogenomic databases

    eggNOGiCOG2123.
    HOGENOMiHOG000229504.
    HOVERGENiHBG051521.
    InParanoidiQ15024.
    KOiK12589.
    OMAiNVENVPC.
    OrthoDBiEOG7H1JKZ.
    PhylomeDBiQ15024.
    TreeFamiTF320641.

    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.
    PF03725. RNase_PH_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF54211. SSF54211. 2 hits.
    SSF55666. SSF55666. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q15024-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASVTLSEAE KVYIVHGVQE DLRVDGRGCE DYRCVEVETD VVSNTSGSAR    50
    VKLGHTDILV GVKAEMGTPK LEKPNEGYLE FFVDCSASAT PEFEGRGGDD 100
    LGTEIANTLY RIFNNKSSVD LKTLCISPRE HCWVLYVDVL LLECGGNLFD 150
    AISIAVKAAL FNTRIPRVRV LEDEEGSKDI ELSDDPYDCI RLSVENVPCI 200
    VTLCKIGYRH VVDATLQEEA CSLASLLVSV TSKGVVTCMR KVGKGSLDPE 250
    SIFEMMETGK RVGKVLHASL QSVVHKEESL GPKRQKVGFL G 291
    Length:291
    Mass (Da):31,821
    Last modified:February 8, 2011 - v3
    Checksum:iA674F745CEC61BBB
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti169 – 1691R → Q.
    Corresponds to variant rs34512144 [ dbSNP | Ensembl ].
    VAR_032765
    Natural varianti274 – 2741V → L.3 Publications
    Corresponds to variant rs6794 [ dbSNP | Ensembl ].
    VAR_014923

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC104165 Genomic DNA. No translation available.
    BC012831 mRNA. Translation: AAH12831.1.
    D29958 mRNA. Translation: BAA06226.1.
    CCDSiCCDS2725.1.
    RefSeqiNP_055819.2. NM_015004.3.
    UniGeneiHs.719958.

    Genome annotation databases

    EnsembliENST00000265564; ENSP00000265564; ENSG00000075914.
    GeneIDi23016.
    KEGGihsa:23016.
    UCSCiuc003coh.1. human.

    Polymorphism databases

    DMDMi322510129.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC104165 Genomic DNA. No translation available.
    BC012831 mRNA. Translation: AAH12831.1 .
    D29958 mRNA. Translation: BAA06226.1 .
    CCDSi CCDS2725.1.
    RefSeqi NP_055819.2. NM_015004.3.
    UniGenei Hs.719958.

    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 E 1-291 [» ]
    ProteinModelPortali Q15024.
    SMRi Q15024. Positions 5-285.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116658. 18 interactions.
    DIPi DIP-31266N.
    IntActi Q15024. 16 interactions.
    MINTi MINT-1457458.
    STRINGi 9606.ENSP00000265564.

    PTM databases

    PhosphoSitei Q15024.

    Polymorphism databases

    DMDMi 322510129.

    2D gel databases

    SWISS-2DPAGE Q15024.

    Proteomic databases

    MaxQBi Q15024.
    PaxDbi Q15024.
    PeptideAtlasi Q15024.
    PRIDEi Q15024.

    Protocols and materials databases

    DNASUi 23016.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000265564 ; ENSP00000265564 ; ENSG00000075914 .
    GeneIDi 23016.
    KEGGi hsa:23016.
    UCSCi uc003coh.1. human.

    Organism-specific databases

    CTDi 23016.
    GeneCardsi GC03P045016.
    H-InvDB HIX0003236.
    HGNCi HGNC:28112. EXOSC7.
    HPAi HPA036182.
    MIMi 606488. gene.
    neXtProti NX_Q15024.
    PharmGKBi PA134880567.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG2123.
    HOGENOMi HOG000229504.
    HOVERGENi HBG051521.
    InParanoidi Q15024.
    KOi K12589.
    OMAi NVENVPC.
    OrthoDBi EOG7H1JKZ.
    PhylomeDBi Q15024.
    TreeFami TF320641.

    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 EXOSC7. human.
    EvolutionaryTracei Q15024.
    GenomeRNAii 23016.
    NextBioi 43952.
    PROi Q15024.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q15024.
    Bgeei Q15024.
    Genevestigatori Q15024.

    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.
    PF03725. RNase_PH_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54211. SSF54211. 2 hits.
    SSF55666. SSF55666. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The DNA sequence, annotation and analysis of human chromosome 3."
      Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J.
      , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
      Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Tissue: Brain.
    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], VARIANT LEU-274.
      Tissue: Brain.
    3. "Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1."
      Nagase T., Miyajima N., Tanaka A., Sazuka T., Seki N., Sato S., Tabata S., Ishikawa K., Kawarabayasi Y., Kotani H., Nomura N.
      DNA Res. 2:37-43(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2-291, VARIANT LEU-274.
      Tissue: Bone marrow.
    4. Bienvenut W.V., Lilla S., von Kriegsheim A., Lempens A., Kolch W.
      Submitted (DEC-2008) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 2-23, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY.
      Tissue: Ovarian carcinoma.
    5. "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.
    6. "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.
    7. "Protein-protein interactions of hCsl4p with other human exosome subunits."
      Raijmakers R., Noordman Y.E., van Venrooij W.J., Pruijn G.J.M.
      J. Mol. Biol. 315:809-818(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, INTERACTION WITH EXOSC1.
    8. "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.
    9. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
      Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
      Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-116, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "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.
    12. "Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation."
      Zhu Y., Chen G., Lv F., Wang X., Ji X., Xu Y., Sun J., Wu L., Zheng Y.T., Gao G.
      Proc. Natl. Acad. Sci. U.S.A. 108:15834-15839(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ZC3HAV1.
    13. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
      Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
      Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "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.
    15. Erratum
      Liu Q., Greimann J.C., Lima C.D.
      Cell 131:188-189(2007)
    16. Cited for: VARIANT [LARGE SCALE ANALYSIS] LEU-274, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiEXOS7_HUMAN
    AccessioniPrimary (citable) accession number: Q15024
    Secondary accession number(s): Q96E72
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 6, 2002
    Last sequence update: February 8, 2011
    Last modified: October 1, 2014
    This is version 139 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, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 3
      Human chromosome 3: 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

    External Data

    Dasty 3