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Q15024

- EXOS7_HUMAN

UniProt

Q15024 - EXOS7_HUMAN

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Protein
Exosome complex component RRP42
Gene
EXOSC7, KIAA0116, RRP42
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.

GO - Molecular functioni

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

GO - Biological processi

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

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134880567.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 291290Exosome complex component RRP42
PRO_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 ZC3HAV1.6 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

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.

Miscellaneous databases

EvolutionaryTraceiQ15024.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.

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...

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 138 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.

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

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