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P34160

- NCBP1_YEAST

UniProt

P34160 - NCBP1_YEAST

Protein

Nuclear cap-binding protein complex subunit 1

Gene

STO1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 136 (01 Oct 2014)
      Sequence version 2 (01 Oct 1996)
      Previous versions | rss
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    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

    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.

    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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

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

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi22 – 309Nuclear localization signalSequence Analysis

    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.Curated
    Contains 1 MIF4G domain.Curated

    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.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti164 – 1641D → V in L27744. (PubMed:10733586)Curated
    Sequence conflicti633 – 6331R → I in L27744. (PubMed:10733586)Curated
    Sequence conflicti704 – 7041A → R in L27744. (PubMed:10733586)Curated

    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

    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: October 1, 2014
    This is version 136 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.1 Publication
    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