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Protein

Nuclear cap-binding protein subunit 2

Gene

CBC2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the CBC complex, which binds co-transcriptionally to the cap of pre-mRNAs and is involved in maturation, export and degradation of nuclear mRNAs. The CBC complex is required for efficient pre-mRNA splicing through efficient commitment complex and spliceosome formation. Together with NPL3, the CBC complex is required for export of mRNAs out of the nucleus. The CBC complex is also involved in nuclear mRNA degradation, probably by directing the mRNAs to the sites of degradation. Affects replication of the positive-strand RNA virus BMV.10 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei24 – 241mRNA capBy similarity
Binding sitei49 – 491mRNA capBy similarity

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • RNA cap binding Source: SGD

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing, mRNA transport, Nonsense-mediated mRNA decay, Transport

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-34073-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-72086. mRNA Capping.
R-SCE-72165. mRNA Splicing - Minor Pathway.
R-SCE-77595. Processing of Intronless Pre-mRNAs.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear cap-binding protein subunit 2
Alternative name(s):
20 kDa nuclear cap-binding protein
NCBP 20 kDa subunit
Short name:
CBP20
Gene namesi
Name:CBC2
Synonyms:CBP20, MUD13, SAE1
Ordered Locus Names:YPL178W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL178W.
SGDiS000006099. CBC2.

Subcellular locationi

GO - Cellular componenti

  • commitment complex Source: SGD
  • nuclear cap binding complex Source: SGD
  • perinuclear region of cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 208208Nuclear cap-binding protein subunit 2PRO_0000232990Add
BLAST

Proteomic databases

MaxQBiQ08920.

Interactioni

Subunit structurei

Component of the nuclear cap-binding complex (CBC), a heterodimer composed of STO1/CBC1 and CBC2 that interacts with capped RNAs. The complex interacts strongly with the importin subunit alpha SRP1. The SRP1-CBC trimer also binds to capped RNAs, but formation of the importin alpha/beta heterodimer upon binding of KAP95 to SRP1 in the cytoplasm causes dissociation of CBC from the RNA. The CBC complex is part of the commitment complex 1 (CC1), binding to the cap of pre-mRNA and interacting with U1 snRNP subunits MUD2 and SNU56. The CBC complex is part of the NRD1 complex, composed of CBC2, NAB1, NRD1, SEN1 and STO1/CBC2. The CBC complex also interacts with NPL3 and eIF4G (TIF4631 and TIF4632).7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SRP1Q028213EBI-33556,EBI-1797
STO1P341607EBI-33556,EBI-745

Protein-protein interaction databases

BioGridi36005. 313 interactions.
DIPiDIP-1117N.
IntActiQ08920. 26 interactions.
MINTiMINT-552911.

Structurei

3D structure databases

ProteinModelPortaliQ08920.
SMRiQ08920. Positions 44-155.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini46 – 12479RRMPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni118 – 1225mRNA cap-bindingBy similarity
Regioni129 – 1335mRNA cap-bindingBy similarity
Regioni139 – 1402mRNA cap-bindingBy similarity

Sequence similaritiesi

Belongs to the RRM NCBP2 family.Curated
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000003197.
HOGENOMiHOG000217589.
InParanoidiQ08920.
KOiK12883.
OMAiRFKFTPC.
OrthoDBiEOG72G1KS.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR027157. NCBP2.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR18847. PTHR18847. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08920-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLEEFDEVK YDHSTKRLDT PSRYLLRKAR RNPNGLQELR ESMKSSTIYV
60 70 80 90 100
GNLSFYTSEE QIYELFSKCG TIKRIIMGLD RFKFTPCGFC FIIYSCPDEA
110 120 130 140 150
LNALKYLSDT KLDEKTITID LDPGFEDGRQ FGRGKSGGQV SDELRFDFDA
160 170 180 190 200
SRGGFAIPFA ERVGVPHSRF DNSSSQSNTN NYIPPPDAMG TFRPGFDEER

EDDNYVPQ
Length:208
Mass (Da):23,774
Last modified:November 1, 1996 - v1
Checksum:iB77E93BDDC429160
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U39665 mRNA. Translation: AAF21454.1.
Z73534 Genomic DNA. Translation: CAA97885.1.
AY692949 Genomic DNA. Translation: AAT92968.1.
BK006949 Genomic DNA. Translation: DAA11256.1.
PIRiS65190.
RefSeqiNP_015147.1. NM_001183992.1.

Genome annotation databases

EnsemblFungiiYPL178W; YPL178W; YPL178W.
GeneIDi855925.
KEGGisce:YPL178W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U39665 mRNA. Translation: AAF21454.1.
Z73534 Genomic DNA. Translation: CAA97885.1.
AY692949 Genomic DNA. Translation: AAT92968.1.
BK006949 Genomic DNA. Translation: DAA11256.1.
PIRiS65190.
RefSeqiNP_015147.1. NM_001183992.1.

3D structure databases

ProteinModelPortaliQ08920.
SMRiQ08920. Positions 44-155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36005. 313 interactions.
DIPiDIP-1117N.
IntActiQ08920. 26 interactions.
MINTiMINT-552911.

Proteomic databases

MaxQBiQ08920.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL178W; YPL178W; YPL178W.
GeneIDi855925.
KEGGisce:YPL178W.

Organism-specific databases

EuPathDBiFungiDB:YPL178W.
SGDiS000006099. CBC2.

Phylogenomic databases

GeneTreeiENSGT00390000003197.
HOGENOMiHOG000217589.
InParanoidiQ08920.
KOiK12883.
OMAiRFKFTPC.
OrthoDBiEOG72G1KS.

Enzyme and pathway databases

BioCyciYEAST:G3O-34073-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-72086. mRNA Capping.
R-SCE-72165. mRNA Splicing - Minor Pathway.
R-SCE-77595. Processing of Intronless Pre-mRNAs.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

PROiQ08920.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR027157. NCBP2.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR18847. PTHR18847. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Importin provides a link between nuclear protein import and U snRNA export."
    Goerlich D., Kraft R., Kostka S., Vogel F., Hartmann E., Laskey R.A., Mattaj I.W., Izaurraide E.
    Cell 87:21-32(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE CBC AND SRP1-CBC COMPLEXES, U SNRNA-BINDING, SUBCELLULAR LOCATION, FUNCTION OF THE CBC AND SRP1-CBC COMPLEXES.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. "The yeast splicing factor Mud13p is a commitment complex component and corresponds to CBP20, the small subunit of the nuclear cap-binding complex."
    Colot H.V., Stutz F., Rosbash M.
    Genes Dev. 10:1699-1708(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE CBC COMPLEX.
  6. "A yeast cap binding protein complex (yCBC) acts at an early step in pre-mRNA splicing."
    Lewis J.D., Goerlich D., Mattaj I.W.
    Nucleic Acids Res. 24:3332-3336(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE CBC COMPLEX.
  7. "Mutations in Saccharomyces cerevisiae that block meiotic prophase chromosome metabolism and confer cell cycle arrest at pachytene identify two new meiosis-specific genes SAE1 and SAE3."
    McKee A.H.Z., Kleckner N.
    Genetics 146:817-834(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Genetic and physical interactions involving the yeast nuclear cap-binding complex."
    Fortes P., Kufel J., Fornerod M., Polycarpou-Schwarz M., Lafontaine D., Tollervey D., Mattaj I.W.
    Mol. Cell. Biol. 19:6543-6553(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH MUD2 AND SNU56, FUNCTION OF THE CBC COMPLEX.
  9. "A generic protein purification method for protein complex characterization and proteome exploration."
    Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Seraphin B.
    Nat. Biotechnol. 17:1030-1032(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CBC COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION OF THE COMPLEX WITH CAPPED RNA.
  10. "7The yeast mRNA-binding protein Npl3p interacts with the cap-binding complex."
    Shen E.C., Stage-Zimmermann T., Chui P., Silver P.A.
    J. Biol. Chem. 275:23718-23724(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH NPL3, FUNCTION.
  11. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  12. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  13. "Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus."
    Kushner D.B., Lindenbach B.D., Grdzelishvili V.Z., Noueiry A.O., Paul S.M., Ahlquist P.
    Proc. Natl. Acad. Sci. U.S.A. 100:15764-15769(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  14. "The interaction of the cap-binding complex (CBC) with eIF4G is dispensable for translation in yeast."
    Baron-Benhamou J., Fortes P., Inada T., Preiss T., Hentze M.W.
    RNA 9:654-662(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE CBC COMPLEX.
  15. "Cap-binding protein 1-mediated and eukaryotic translation initiation factor 4E-mediated pioneer rounds of translation in yeast."
    Gao Q., Das B., Sherman F., Maquat L.E.
    Proc. Natl. Acad. Sci. U.S.A. 102:4258-4263(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  16. "A nuclear degradation pathway controls the abundance of normal mRNAs in Saccharomyces cerevisiae."
    Kuai L., Das B., Sherman F.
    Proc. Natl. Acad. Sci. U.S.A. 102:13962-13967(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  17. "Subunit architecture of multimeric complexes isolated directly from cells."
    Hernandez H., Dziembowski A., Taverner T., Seraphin B., Robinson C.V.
    EMBO Rep. 7:605-610(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CBC COMPLEX, INTERACTION WITH SRP1, IDENTIFICATION BY MASS SPECTROMETRY.
  18. "Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts."
    Vasiljeva L., Buratowski S.
    Mol. Cell 21:239-248(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN NRD1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  19. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNCBP2_YEAST
AccessioniPrimary (citable) accession number: Q08920
Secondary accession number(s): D6W3J0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

In contrast to metazoans, where the CBC complex is involved in the nuclear export of capped U snRNAs, it is believed that in yeast, U snRNAs are not exported from the nucleus and U snRNPs are assembled in the nucleus from RNAs and imported proteins.
Present with 6200 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.