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P34160

- NCBP1_YEAST

UniProt

P34160 - NCBP1_YEAST

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Protein

Nuclear cap-binding protein complex subunit 1

Gene
STO1, CBC1, CBP80, GCR3, SUT1, YMR125W, YM8564.07, YM9553.01
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Component of the CBC complex, which binds co-transcriptionally to the 5'-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.13 Publications

GO - Molecular functioni

  1. mRNA binding Source: SGD
  2. protein binding Source: IntAct
  3. RNA cap binding Source: InterPro

GO - Biological processi

  1. 7-methylguanosine mRNA capping Source: UniProtKB-KW
  2. mRNA cis splicing, via spliceosome Source: InterPro
  3. mRNA splicing, via spliceosome Source: SGD
  4. mRNA transport Source: UniProtKB-KW
  5. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: SGD
  6. response to osmotic stress Source: SGD
Complete GO annotation...

Keywords - Biological processi

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

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-32818-MONOMER.
ReactomeiREACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_191540. mRNA Splicing - Minor Pathway.
REACT_191574. Processing of Intronless Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear cap-binding protein complex subunit 1
Alternative name(s):
80 kDa nuclear cap-binding protein
Short name:
CBP80
Short name:
NCBP 80 kDa subunit
Glycolysis regulation protein 3
Protein SUT1
Suppressor of TOP1 protein
Gene namesi
Name:STO1
Synonyms:CBC1, CBP80, GCR3, SUT1
Ordered Locus Names:YMR125W
ORF Names:YM8564.07, YM9553.01
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XIII

Organism-specific databases

CYGDiYMR125w2.
SGDiS000004732. STO1.

Subcellular locationi

Nucleus. Cytoplasmperinuclear region
Note: Predominantly nuclear, is able to exit the nucleus in an RNA-dependent manner.3 Publications

GO - Cellular componenti

  1. commitment complex Source: SGD
  2. nuclear cap binding complex Source: SGD
  3. perinuclear region of cytoplasm Source: UniProtKB-SubCell
  4. polysome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 861861Nuclear cap-binding protein complex subunit 1PRO_0000087447Add
BLAST

Proteomic databases

MaxQBiP34160.
PaxDbiP34160.
PeptideAtlasiP34160.

Expressioni

Gene expression databases

GenevestigatoriP34160.

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).8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CBC2Q089207EBI-745,EBI-33556

Protein-protein interaction databases

BioGridi35302. 177 interactions.
DIPiDIP-4434N.
IntActiP34160. 53 interactions.
MINTiMINT-552943.
STRINGi4932.YMR125W.

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3UKYX-ray2.35C1-30[»]
ProteinModelPortaliP34160.
SMRiP34160. Positions 397-722.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini36 – 264229MIF4GAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi22 – 309Nuclear localization signal Reviewed prediction

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi774 – 80128Asp/Glu-rich (acidic)Add
BLAST
Compositional biasi802 – 82524Arg/Lys-rich (basic)Add
BLAST

Sequence similaritiesi

Belongs to the NCBP1 family.
Contains 1 MIF4G domain.

Phylogenomic databases

eggNOGiNOG303489.
GeneTreeiENSGT00390000001733.
HOGENOMiHOG000066047.
KOiK12882.
OMAiTWKWAEW.
OrthoDBiEOG7MKWFF.

Family and domain databases

Gene3Di1.25.40.180. 3 hits.
InterProiIPR016024. ARM-type_fold.
IPR027159. CBP80.
IPR016021. MIF4-like_typ_1/2/3.
IPR015172. MIF4G-like_typ-1.
IPR015174. MIF4G-like_typ-2.
IPR003890. MIF4G-like_typ-3.
[Graphical view]
PANTHERiPTHR12412. PTHR12412. 1 hit.
PfamiPF02854. MIF4G. 1 hit.
PF09088. MIF4G_like. 1 hit.
PF09090. MIF4G_like_2. 1 hit.
[Graphical view]
SMARTiSM00543. MIF4G. 1 hit.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 3 hits.

Sequencei

Sequence statusi: Complete.

P34160-1 [UniParc]FASTAAdd to Basket

« Hide

MFNRKRRGDF DEDENYRDFR PRMPKRQRIP PVVQLCKEMM PDIRTIGESV    50
KAFEDDIKFL SEAIMNEYGH EDYFNNALLS TLNAVVVEQP QKQAAIALLT 100
MVVNSKNNVA GKSIINYFFE ELQKWCKQTY NDEFKSTSNE TGPWNKIKLI 150
LRFLSILSPM FLVDELINIY KSLFELSIEL NNLDPGNRVP LSEAIYTNTL 200
LNIPYLFFFN RNNDGLRTKV EELLAYVEQN YLVKTTDINL LREYNGEPPY 250
EMVELVRVVL PNVKKALINN LEQLNELFPD WNHLLTPQTG DEGFNDALTL 300
PSVDDLKSFV RLNKNFGSVD SMWKTPRYAF HVYLPNSAGN FETVVPISTY 350
AGQLFNDIII DLVESLEFNR KEVARQVITL DLFFKAGIFT EPGESIAQLI 400
ATYEENPLAP TFKIEDLAIE TILGLIFKLP SVSQPFAYFY TLLVDICQNS 450
PKAIAPVFGR AFRFFYSHLD SLDFELKLRY LDWFSIQMSN FNFSWKWNEW 500
EDDSIKFGKY FYNPKVNFAK NLIQKELRLT SNFSEVEDSL PQEFTKYLDT 550
SYIPRDQLIN YYQSLFTGYT VEEDSVRKND LYFRQEGVPM ENTVRKILDY 600
THKANNSREV TELESILGEL KNEYGSIISD FNRFVIILLV QAVTDSGSRS 650
LSHANKYIND LKEDLKTIFA KIELDIETKE YIIIEAVLTF WNANPQTGFL 700
VADAFKYAGL LTSRTIFTFI FNETGLKNNG LIEATAIEAV FRNLSQQISE 750
ENESGNNFEF VFERLCTIAN STIDLLDVNA DEDIEIPKVN GEMDIDDIED 800
DKLDLKWKYF TVIGFIKSIL RRYSHEYREL ADKFIANIDN AIPHESTRRT 850
ISNWIQETKE V 861
Length:861
Mass (Da):100,018
Last modified:October 1, 1996 - v2
Checksum:iEDD04907BDC9207D
GO

Sequence cautioni

The sequence L27744 differs from that shown. Reason: Frameshift at position 708.
The sequence BAA01076.1 differs from that shown. Reason: Erroneous gene model prediction.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti164 – 1641D → V in L27744. 1 Publication
Sequence conflicti633 – 6331R → I in L27744. 1 Publication
Sequence conflicti704 – 7041A → R in L27744. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D10224 Genomic DNA. Translation: BAA01076.1. Sequence problems.
L07650 Genomic DNA. No translation available.
L27744 Genomic DNA. No translation available.
Z49273 Genomic DNA. Translation: CAA89274.1.
Z48622 Genomic DNA. Translation: CAA88550.1.
BK006946 Genomic DNA. Translation: DAA10022.1.
PIRiA44919.
RefSeqiNP_013844.2. NM_001182626.1.

Genome annotation databases

EnsemblFungiiYMR125W; YMR125W; YMR125W.
GeneIDi855155.
KEGGisce:YMR125W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D10224 Genomic DNA. Translation: BAA01076.1 . Sequence problems.
L07650 Genomic DNA. No translation available.
L27744 Genomic DNA. No translation available.
Z49273 Genomic DNA. Translation: CAA89274.1 .
Z48622 Genomic DNA. Translation: CAA88550.1 .
BK006946 Genomic DNA. Translation: DAA10022.1 .
PIRi A44919.
RefSeqi NP_013844.2. NM_001182626.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3UKY X-ray 2.35 C 1-30 [» ]
ProteinModelPortali P34160.
SMRi P34160. Positions 397-722.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 35302. 177 interactions.
DIPi DIP-4434N.
IntActi P34160. 53 interactions.
MINTi MINT-552943.
STRINGi 4932.YMR125W.

Proteomic databases

MaxQBi P34160.
PaxDbi P34160.
PeptideAtlasi P34160.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YMR125W ; YMR125W ; YMR125W .
GeneIDi 855155.
KEGGi sce:YMR125W.

Organism-specific databases

CYGDi YMR125w2.
SGDi S000004732. STO1.

Phylogenomic databases

eggNOGi NOG303489.
GeneTreei ENSGT00390000001733.
HOGENOMi HOG000066047.
KOi K12882.
OMAi TWKWAEW.
OrthoDBi EOG7MKWFF.

Enzyme and pathway databases

BioCyci YEAST:G3O-32818-MONOMER.
Reactomei REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_191540. mRNA Splicing - Minor Pathway.
REACT_191574. Processing of Intronless Pre-mRNAs.

Miscellaneous databases

NextBioi 978566.

Gene expression databases

Genevestigatori P34160.

Family and domain databases

Gene3Di 1.25.40.180. 3 hits.
InterProi IPR016024. ARM-type_fold.
IPR027159. CBP80.
IPR016021. MIF4-like_typ_1/2/3.
IPR015172. MIF4G-like_typ-1.
IPR015174. MIF4G-like_typ-2.
IPR003890. MIF4G-like_typ-3.
[Graphical view ]
PANTHERi PTHR12412. PTHR12412. 1 hit.
Pfami PF02854. MIF4G. 1 hit.
PF09088. MIF4G_like. 1 hit.
PF09090. MIF4G_like_2. 1 hit.
[Graphical view ]
SMARTi SM00543. MIF4G. 1 hit.
[Graphical view ]
SUPFAMi SSF48371. SSF48371. 3 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "GCR3 encodes an acidic protein that is required for expression of glycolytic genes in Saccharomyces cerevisiae."
    Uemura H., Jigami Y.
    J. Bacteriol. 174:5526-5532(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  2. "Mutations in GCR3, a gene involved in the expression of glycolytic genes in Saccharomyces cerevisiae, suppress the temperature-sensitive growth of hpr1 mutants."
    Uemura H., Pandit S., Jigami Y., Sternglanz R.
    Genetics 142:1095-1103(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  3. "The role of nuclear cap binding protein Cbc1p of yeast in mRNA termination and degradation."
    Das B., Guo Z., Russo P., Chartrand P., Sherman F.
    Mol. Cell. Biol. 20:2827-2838(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], IDENTIFICATION OF INTRON, FUNCTION, SUBCELLULAR LOCATION.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "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: PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE CBC AND SRP1-CBC COMPLEXES, U SNRNA-BINDING, SUBCELLULAR LOCATION, FUNCTION OF THE CBC AND SRP1-CBC COMPLEXES.
  7. "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.
  8. "Arginine methylation facilitates the nuclear export of hnRNP proteins."
    Shen E.C., Henry M.F., Weiss V.H., Valentini S.R., Silver P.A., Lee M.S.
    Genes Dev. 12:679-691(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex."
    Zhang D., Rosbash M.
    Genes Dev. 13:581-592(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PRE-MRNA IN THE COMMITMENT COMPLEX.
  10. "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.
  11. "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.
  12. "Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system."
    Aravind L., Koonin E.V.
    Genome Res. 10:1172-1184(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN.
  13. "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, SUBCELLULAR LOCATION, FUNCTION.
  14. "The yeast nuclear cap binding complex can interact with translation factor eIF4G and mediate translation initiation."
    Fortes P., Inada T., Preiss T., Hentze M.W., Mattaj I.W., Sachs A.B.
    Mol. Cell 6:191-196(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH EIF4G.
  15. "Degradation of normal mRNA in the nucleus of Saccharomyces cerevisiae."
    Das B., Butler J.S., Sherman F.
    Mol. Cell. Biol. 23:5502-5515(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  16. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  17. "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.
  18. "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.
  19. "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.
  20. "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.
  21. "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.
  22. "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.

Entry informationi

Entry nameiNCBP1_YEAST
AccessioniPrimary (citable) accession number: P34160
Secondary accession number(s): D6VZU8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: October 1, 1996
Last modified: September 3, 2014
This is version 135 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 11300 molecules/cell in log phase SD medium.
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.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

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

External Data

Dasty 3

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