Nuclear cap-binding protein complex subunit 1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P34160 (NCBP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 122. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	STO1
Synonyms:	CBC1, CBP80, GCR3, SUT1
Ordered Locus Names:	YMR125W
ORF Names:	YM8564.07, YM9553.01

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	861 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.1 Ref.2 Ref.3 Ref.6 Ref.7 Ref.8 Ref.10 Ref.13 Ref.15 Ref.17 Ref.18 Ref.19 Ref.20
Subunit structure	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). Ref.6 Ref.9 Ref.10 Ref.11 Ref.13 Ref.14 Ref.21 Ref.22
Subcellular location	Nucleus. Cytoplasm › perinuclear region. Note: Predominantly nuclear, is able to exit the nucleus in an RNA-dependent manner. Ref.3 Ref.6 Ref.13
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.
Sequence similarities	Belongs to the NCBP1 family. Contains 1 MIF4G domain.
Sequence caution	The sequence BAA01076.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence L27744 differs from that shown. Reason: Frameshift at position 708.

Ontologies

Keywords
Biological process	Nonsense-mediated mRNA decay Transport mRNA capping mRNA processing mRNA splicing mRNA transport
Cellular component	Cytoplasm Nucleus
Ligand	RNA-binding
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	7-methylguanosine mRNA capping Inferred from electronic annotation. Source: UniProtKB-KW mRNA cis splicing, via spliceosome Inferred from electronic annotation. Source: InterPro mRNA splicing, via spliceosome Inferred from physical interaction Ref.9. Source: SGD mRNA transport Inferred from electronic annotation. Source: UniProtKB-KW nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Inferred from direct assay Ref.19. Source: SGD response to osmotic stress Inferred from mutant phenotype PubMed 22072789. Source: SGD
Cellular_component	commitment complex Inferred from physical interaction Ref.9. Source: SGD nuclear cap binding complex Inferred from direct assay Ref.7. Source: SGD perinuclear region of cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell polysome Inferred from direct assay PubMed 22072789. Source: SGD
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro RNA cap binding Inferred from electronic annotation. Source: InterPro mRNA binding Inferred from physical interaction Ref.9. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CBC2	Q08920	6	EBI-745,EBI-33556

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 861

861

Nuclear cap-binding protein complex subunit 1

PRO_0000087447

Regions

Domain

36 – 264

229

MIF4G

Motif

22 – 30

Nuclear localization signal Potential

Compositional bias

774 – 801

Asp/Glu-rich (acidic)

Compositional bias

802 – 825

Arg/Lys-rich (basic)

Experimental info

Sequence conflict

164

D → V in L27744. Ref.3

Sequence conflict

633

R → I in L27744. Ref.3

Sequence conflict

704

A → R in L27744. Ref.3

Sequences

Sequence

Length

Mass (Da)

Tools

P34160 [UniParc].

Last modified October 1, 1996. Version 2.
Checksum: EDD04907BDC9207D
Show »

FASTA

861

100,018

        10         20         30         40         50         60 
MFNRKRRGDF DEDENYRDFR PRMPKRQRIP PVVQLCKEMM PDIRTIGESV KAFEDDIKFL 

        70         80         90        100        110        120 
SEAIMNEYGH EDYFNNALLS TLNAVVVEQP QKQAAIALLT MVVNSKNNVA GKSIINYFFE 

       130        140        150        160        170        180 
ELQKWCKQTY NDEFKSTSNE TGPWNKIKLI LRFLSILSPM FLVDELINIY KSLFELSIEL 

       190        200        210        220        230        240 
NNLDPGNRVP LSEAIYTNTL LNIPYLFFFN RNNDGLRTKV EELLAYVEQN YLVKTTDINL 

       250        260        270        280        290        300 
LREYNGEPPY EMVELVRVVL PNVKKALINN LEQLNELFPD WNHLLTPQTG DEGFNDALTL 

       310        320        330        340        350        360 
PSVDDLKSFV RLNKNFGSVD SMWKTPRYAF HVYLPNSAGN FETVVPISTY AGQLFNDIII 

       370        380        390        400        410        420 
DLVESLEFNR KEVARQVITL DLFFKAGIFT EPGESIAQLI ATYEENPLAP TFKIEDLAIE 

       430        440        450        460        470        480 
TILGLIFKLP SVSQPFAYFY TLLVDICQNS PKAIAPVFGR AFRFFYSHLD SLDFELKLRY 

       490        500        510        520        530        540 
LDWFSIQMSN FNFSWKWNEW EDDSIKFGKY FYNPKVNFAK NLIQKELRLT SNFSEVEDSL 

       550        560        570        580        590        600 
PQEFTKYLDT SYIPRDQLIN YYQSLFTGYT VEEDSVRKND LYFRQEGVPM ENTVRKILDY 

       610        620        630        640        650        660 
THKANNSREV TELESILGEL KNEYGSIISD FNRFVIILLV QAVTDSGSRS LSHANKYIND 

       670        680        690        700        710        720 
LKEDLKTIFA KIELDIETKE YIIIEAVLTF WNANPQTGFL VADAFKYAGL LTSRTIFTFI 

       730        740        750        760        770        780 
FNETGLKNNG LIEATAIEAV FRNLSQQISE ENESGNNFEF VFERLCTIAN STIDLLDVNA 

       790        800        810        820        830        840 
DEDIEIPKVN GEMDIDDIED DKLDLKWKYF TVIGFIKSIL RRYSHEYREL ADKFIANIDN 

       850        860 
AIPHESTRRT ISNWIQETKE V

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. Barrell B.G. Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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, 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]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] 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, 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, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

A44919.

RefSeq

NP_013844.2. NM_001182626.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3UKY	X-ray	2.35	C	1-30	[»]

ProteinModelPortal

P34160.

SMR

P34160. Positions 397-722.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4434N.

IntAct

P34160. 53 interactions.

MINT

MINT-552943.

STRING

4932.YMR125W.

Proteomic databases

PaxDb

P34160.

PeptideAtlas

P34160.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YMR125W; YMR125W; YMR125W.

GeneID

855155.

KEGG

sce:YMR125W.

Organism-specific databases

CYGD

YMR125w2.

SGD

S000004732. STO1.

Phylogenomic databases

eggNOG

NOG303489.

GeneTree

ENSGT00390000001733.

HOGENOM

HOG000066047.

K12882.

OMA

RSLSHAN.

OrthoDB

EOG44J5S6.

Gene expression databases

Genevestigator

P34160.

GermOnline

YMR125W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

1.25.40.180. 3 hits.

InterPro

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]

PANTHER

PTHR12412. PTHR12412. 1 hit.

Pfam

PF02854. MIF4G. 1 hit.
PF09088. MIF4G_like. 1 hit.
PF09090. MIF4G_like_2. 1 hit.
[Graphical view]

SMART

SM00543. MIF4G. 1 hit.
[Graphical view]

SUPFAM

SSF48371. ARM-type_fold. 3 hits.

ProtoNet

Search...

Other

NextBio

978566.

Entry information

Entry name

NCBP1_YEAST

Accession

Primary (citable) accession number: P34160
Secondary accession number(s): D6VZU8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	October 1, 1996
Last modified:	May 1, 2013
This is version 122 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome XIII

Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents