Q9Y3B2 (EXOS1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component CSL4

Alternative name(s):
Exosome component 1

Gene names

Name:	EXOSC1
Synonyms:	CSL4
ORF Names:	CGI-108

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	195 AA.
Sequence status	Complete.
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 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. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.
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 EXOSC5, EXOSC7 and EXOSC10. Interacts with DDX60. Ref.6 Ref.7 Ref.8 Ref.9 Ref.12 Ref.15
Subcellular location	Nucleus › nucleolus. Nucleus Probable. Cytoplasm Probable Ref.8.
Sequence similarities	Contains 1 S1 motif domain.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Ligand	RNA-binding
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Traceable author statement. Source: Reactome gene expression Traceable author statement. Source: Reactome rRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytosol Traceable author statement. Source: Reactome exosome (RNase complex) Inferred from direct assay Ref.12. Source: UniProtKB nucleolus Inferred from direct assay Ref.8. Source: UniProtKB
Molecular_function	RNA binding Non-traceable author statement Ref.8. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
EXOSC4	Q9NPD3	3	EBI-371892,EBI-371823
EXOSC5	Q9NQT4	10	EBI-371892,EBI-371876
EXOSC7	Q15024	6	EBI-371892,EBI-371841

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 195

195

Exosome complex component CSL4

PRO_0000087127

Regions

Domain

66 – 147

82

S1 motif

Amino acid modifications

Modified residue

21

1

Phosphoserine Ref.10 Ref.11 Ref.13

Secondary structure

1

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195

Helix Strand Turn

Details...

Beta strand

13 – 16

4

Turn

17 – 19

3

Beta strand

23 – 25

3

Beta strand

27 – 29

3

Beta strand

32 – 34

3

Beta strand

41 – 45

5

Beta strand

49 – 52

4

Beta strand

70 – 78

9

Beta strand

80 – 93

14

Beta strand

103 – 106

4

Helix

107 – 109

3

Helix

118 – 120

3

Beta strand

124 – 135

12

Beta strand

142 – 145

4

Beta strand

148 – 150

3

Beta strand

159 – 161

3

Beta strand

165 – 168

4

Beta strand

171 – 173

3

Turn

175 – 178

4

Sequences

	Sequence		Length	Mass (Da)
	Q9Y3B2 [UniParc]. Last modified November 1, 1999. Version 1. Checksum: E9C3B0A66F911195	FASTA	195	21,452
	10 20 30 40 50 60 MAPPVRYCIP GERLCNLEEG SPGSGTYTRH GYIFSSLAGC LMKSSENGAL PVVSVVRETE 70 80 90 100 110 120 SQLLPDVGAI VTCKVSSINS RFAKVHILYV GSMPLKNSFR GTIRKEDVRA TEKDKVEIYK 130 140 150 160 170 180 SFRPGDIVLA KVISLGDAQS NYLLTTAENE LGVVVAHSES GIQMVPISWC EMQCPKTHTK 190 EFRKVARVQP EFLQT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics." Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C. Genome Res. 10:703-713(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"The DNA sequence and comparative analysis of human chromosome 10." Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J. Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"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: Brain.
[6]	"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.
[7]	"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.
[8]	"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 EXOSC5; EXOSC7 AND EXOSC10.
[9]	"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.
[10]	"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle." Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M. Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[11]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[12]	"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, MASS SPECTROMETRY.
[13]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-21, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[14]	"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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]	"DDX60, a DEXD/H box helicase, is a novel antiviral factor promoting RIG-I-like receptor-mediated signaling." Miyashita M., Oshiumi H., Matsumoto M., Seya T. Mol. Cell. Biol. 31:3802-3819(2011) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH DDX60.
[16]	"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), RECONSTITUTION OF THE RNA EXOSOME CORE COMPLEX.
[17]	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

AF151866 mRNA. Translation: AAD34103.1.
AK313717 mRNA. Translation: BAG36460.1.
AL355490 Genomic DNA. Translation: CAI40782.1.
CH471066 Genomic DNA. Translation: EAW49936.1.
BC022067 mRNA. Translation: AAH22067.1.

IPI

IPI00032823.

RefSeq

NP_057130.1. NM_016046.3.

UniGene

Hs.632089.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2NN6	X-ray	3.35	I	1-195	[»]

ProteinModelPortal

Q9Y3B2.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9Y3B2. 22 interactions.

STRING

9606.ENSP00000359939.

PTM databases

PhosphoSite

Q9Y3B2.

Polymorphism databases

DMDM

14285410.

Proteomic databases

PaxDb

Q9Y3B2.

PRIDE

Q9Y3B2.

Protocols and materials databases

DNASU

51013.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000370902; ENSP00000359939; ENSG00000171311.

GeneID

51013.

KEGG

hsa:51013.

UCSC

uc001kni.3. human.

Organism-specific databases

CTD

51013.

GeneCards

GC10M099191.

HGNC

HGNC:17286. EXOSC1.

HPA

HPA038370.

MIM

606493. gene.

neXtProt

NX_Q9Y3B2.

PharmGKB

PA134900737.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1096.

HOGENOM

HOG000177330.

HOVERGEN

HBG051516.

InParanoid

Q9Y3B2.

KO

K07573.

OMA

AGCLTKS.

OrthoDB

EOG40ZQZP.

PhylomeDB

Q9Y3B2.

Enzyme and pathway databases

Reactome

REACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

Q9Y3B2.

Bgee

Q9Y3B2.

CleanEx

HS_EXOSC1.

Genevestigator

Q9Y3B2.

GermOnline

ENSG00000171311. Homo sapiens.

Family and domain databases

InterPro

IPR019495. EXOSC1.
IPR025721. Exosome_cplx_N_dom.
IPR022967. RNA-binding_domain_S1.
[Graphical view]

Pfam

PF14382. ECR1_N. 1 hit.
PF10447. EXOSC1. 1 hit.
[Graphical view]

SMART

SM00316. S1. 1 hit.
[Graphical view]

PROSITE

PS50126. S1. False negative.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9Y3B2.

GenomeRNAi

51013.

NextBio

53508.

SOURCE

Search...

Entry information

Entry name

EXOS1_HUMAN

Accession

Primary (citable) accession number: Q9Y3B2
Secondary accession number(s): B2R9B3, Q5JTH3

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 2001
Last sequence update:	November 1, 1999
Last modified:	May 1, 2013
This is version 116 of the entry and version 1 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.