Q15024 (EXOS7_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component RRP42

Alternative name(s):
Exosome component 7
Ribosomal RNA-processing protein 42
p8

Gene names

Name:	EXOSC7
Synonyms:	KIAA0116, RRP42

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	291 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 anti-sense 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.
Subunit structure	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. Ref.6 Ref.7 Ref.8
Subcellular location	Nucleus › nucleolus. Cytoplasm Probable. Nucleus Probable Ref.7.
Sequence similarities	Belongs to the RNase PH family.
Caution	The six exosome core subunits containing a RNase PH-domain are not phosphorolytically active.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Coding sequence diversity	Polymorphism
Ligand	RNA-binding
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Traceable author statement. Source: Reactome rRNA processing Traceable author statement. Source: UniProtKB
Cellular component	cytosol Traceable author statement. Source: Reactome exosome (RNase complex) Inferred from direct assay Ref.11. Source: UniProtKB nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	3'-5'-exoribonuclease activity Traceable author statement. Source: UniProtKB RNA binding Traceable author statement. Source: UniProtKB protein binding Inferred from physical interaction Ref.7. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
EXOSC1	Q9Y3B2	6	EBI-371841,EBI-371892
EXOSC2	Q13868	5	EBI-371841,EBI-301735

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4

Chain

2 – 291

290

Exosome complex component RRP42

PRO_0000139963

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.4 Ref.10

Modified residue

116

1

N6-acetyllysine Ref.9

Natural variations

Natural variant

169

1

R → Q.
Corresponds to variant rs34512144 [ dbSNP | Ensembl ].

VAR_032765

Natural variant

274

1

V → L. Ref.2 Ref.3
Corresponds to variant rs6794 [ dbSNP | Ensembl ].

VAR_014923

Secondary structure

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291

Helix Strand Turn

Details...

Helix

8 – 15

8

Beta strand

36 – 39

4

Beta strand

49 – 52

4

Beta strand

57 – 60

4

Beta strand

71 – 73

3

Beta strand

79 – 82

4

Turn

87 – 89

3

Helix

104 – 115

12

Beta strand

121 – 124

4

Turn

128 – 130

3

Beta strand

135 – 138

4

Helix

148 – 158

11

Turn

159 – 162

4

Beta strand

167 – 171

5

Beta strand

180 – 186

7

Beta strand

201 – 205

5

Beta strand

210 – 213

4

Helix

216 – 219

4

Beta strand

225 – 228

4

Beta strand

240 – 242

3

Helix

249 – 257

9

Helix

265 – 278

14

Sequences

	Sequence		Length	Mass (Da)
	Q15024 [UniParc]. Last modified February 8, 2011. Version 3. Checksum: A674F745CEC61BBB	FASTA	291	31,821
	10 20 30 40 50 60 MASVTLSEAE KVYIVHGVQE DLRVDGRGCE DYRCVEVETD VVSNTSGSAR VKLGHTDILV 70 80 90 100 110 120 GVKAEMGTPK LEKPNEGYLE FFVDCSASAT PEFEGRGGDD LGTEIANTLY RIFNNKSSVD 130 140 150 160 170 180 LKTLCISPRE HCWVLYVDVL LLECGGNLFD AISIAVKAAL FNTRIPRVRV LEDEEGSKDI 190 200 210 220 230 240 ELSDDPYDCI RLSVENVPCI VTLCKIGYRH VVDATLQEEA CSLASLLVSV TSKGVVTCMR 250 260 270 280 290 KVGKGSLDPE SIFEMMETGK RVGKVLHASL QSVVHKEESL GPKRQKVGFL G

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 16641997] [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: 15489334] [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: 7788527] [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, 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: 11719186] [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: 12419256] [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: 11812149] [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: 15231747] [Abstract] Cited for: PROTEIN INTERACTION.
[9]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-116, MASS SPECTROMETRY.
[10]	"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: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[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: 20531389] [Abstract] Cited for: IDENTIFICATION IN THE RNA EXOSOME COMPLEX, MASS SPECTROMETRY.
[12]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]	"Reconstitution, activities, and structure of the eukaryotic RNA exosome." Liu Q., Greimann J.C., Lima C.D. Cell 127:1223-1237(2006) [PubMed: 17174896] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.35 ANGSTROMS), LACK OF CATALYTIC ACTIVITY, RECONSTITUTION OF THE RNA EXOSOME CORE COMPLEX.
[14]	Erratum Liu Q., Greimann J.C., Lima C.D. Cell 131:188-189(2007)
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AC104165 Genomic DNA. No translation available.
BC012831 mRNA. Translation: AAH12831.1.
D29958 mRNA. Translation: BAA06226.1.

IPI

IPI00014198.

RefSeq

NP_055819.2. NM_015004.3.

UniGene

Hs.719958.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2NN6	X-ray	3.35	E	1-291	[»]

ProteinModelPortal

Q15024.

SMR

Q15024. Positions 5-285.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q15024. 17 interactions.

MINT

MINT-1457458.

STRING

Q15024.

PTM databases

PhosphoSite

Q15024.

Polymorphism databases

DMDM

21362903.

2D gel databases

SWISS-2DPAGE

Q15024.

Proteomic databases

PeptideAtlas

Q15024.

PRIDE

Q15024.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000265564; ENSP00000265564; ENSG00000075914.

GeneID

23016.

KEGG

hsa:23016.

Organism-specific databases

CTD

23016.

GeneCards

GC03P045016.

H-InvDB

HIX0003236.

HGNC

HGNC:28112. EXOSC7.

HPA

HPA036182.

MIM

606488. gene.

neXtProt

NX_Q15024.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG07468.

GeneTree

ENSGT00530000063093.

HOGENOM

HBG737187.

HOVERGEN

HBG051521.

InParanoid

Q15024.

OMA

GRSCEDY.

OrthoDB

EOG47SSF7.

PhylomeDB

Q15024.

Enzyme and pathway databases

Reactome

REACT_111217. Metabolism.

Gene expression databases

ArrayExpress

Q15024.

Bgee

Q15024.

Genevestigator

Q15024.

GermOnline

ENSG00000075914. Homo sapiens.

Family and domain databases

InterPro

IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]

KO

K12589.

Pfam

PF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]

SUPFAM

SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.

ProtoNet

Search...

Other

SOURCE

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Entry information

Entry name

EXOS7_HUMAN

Accession

Primary (citable) accession number: Q15024
Secondary accession number(s): Q96E72

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 6, 2002
Last sequence update:	February 8, 2011
Last modified:	January 25, 2012
This is version 115 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.