Q3UYV9 (NCBP1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nuclear cap-binding protein subunit 1

Alternative name(s):
80 kDa nuclear cap-binding protein
Short name=CBP80
Short name=NCBP 80 kDa subunit

Gene names

Name:	Ncbp1
Synonyms:	Cbp80

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	790 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the cap-binding complex (CBC), which binds cotranscriptionally to the 5'-cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense-mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus via its interaction with ALYREF/THOC4/ALY, leading to the recruitment of the mRNA export machinery to the 5'-end of mRNA and to mRNA export in a 5' to 3' direction through the nuclear pore. The CBC complex is also involved in mediating U snRNA and intronless mRNAs export from the nucleus. The CBC complex is essential for a pioneer round of mRNA translation, before steady state translation when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA translation mediated by the CBC complex plays a central role in nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAs containing at least one exon-junction complex (EJC) via its interaction with UPF1, promoting the interaction between UPF1 and UPF2. The CBC complex is also involved in 'failsafe' NMD, which is independent of the EJC complex, while it does not participate in Staufen-mediated mRNA decay (SMD). During cell proliferation, the CBC complex is also involved in microRNAs (miRNAs) biogenesis via its interaction with SRRT/ARS2 and is required for miRNA-mediated RNA interference. The CBC complex also acts as a negative regulator of PARN, thereby acting as an inhibitor of mRNA deadenylation. In the CBC complex, NCBP1/CBP80 does not bind directly capped RNAs (m7GpppG-capped RNA) but is required to stabilize the movement of the N-terminal loop of NCBP2/CBP20 and lock the CBC into a high affinity cap-binding state with the cap structure. Ref.8
Subunit structure	Component of the nuclear cap-binding complex (CBC), a heterodimer composed of NCBP1/CBP80 and NCBP2/CBP20 that interacts with m7GpppG-capped RNA. Heterodimer with NCBP2. Is part of the exon junction complex (EJC) containing NCBP1, NCBP2, RNPS1, RBM8A, SRRM1, NXF1, UPF3B, UPF2, ALYREF/THOC4 and/or REFBP2. Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and untranslated mRNAs. Interacts with SRRT/ARS2, EIF4G2, HNRNPF, IGF2BP1, HNRNPH1, KIAA0427/CTIF, PARN, DROSHA, UPF1 and ALYREF/THOC4. May interact with EIF4G1; the interaction is however controversial By similarity. Found in a U snRNA export complex with RNUXA/PHAX, NCBP1/CBP80, NCBP2/CBP20, RAN, XPO1 and m7G-capped RNA. Interaction with RNUXA/PHAX. Ref.5 Ref.6 Ref.8
Subcellular location	Nucleus By similarity. Cytoplasm By similarity. Note: Localized in cytoplasmic mRNP granules containing untranslated mRNAs By similarity.
Sequence similarities	Belongs to the NCBP1 family. Contains 1 MIF4G domain.

Ontologies

Keywords
Biological process	Nonsense-mediated mRNA decay RNA-mediated gene silencing Translation regulation Transport mRNA capping mRNA processing mRNA splicing mRNA transport
Cellular component	Cytoplasm Nucleus
Domain	Coiled coil
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	7-methylguanosine mRNA capping Inferred from sequence or structural similarity. Source: UniProtKB gene silencing by RNA Inferred from electronic annotation. Source: UniProtKB-KW mRNA cis splicing, via spliceosome Inferred from electronic annotation. Source: InterPro mRNA cleavage Inferred from sequence or structural similarity. Source: UniProtKB mRNA export from nucleus Inferred from sequence or structural similarity. Source: UniProtKB nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of mRNA 3'-end processing Inferred from sequence or structural similarity. Source: UniProtKB regulation of translational initiation Inferred from sequence or structural similarity. Source: UniProtKB
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell mRNA cap binding complex Inferred from sequence or structural similarity. Source: UniProtKB nuclear cap binding complex Inferred from electronic annotation. Source: InterPro nucleus Inferred from sequence or structural similarity. Source: UniProtKB ribonucleoprotein complex Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro RNA cap binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 790	790	Nuclear cap-binding protein subunit 1		PRO_0000239779
Regions
	Domain	28 – 240	213	MIF4G
	Coiled coil	643 – 713	71	Potential
	Motif	3 – 20	18	Nuclear localization signal Potential
Amino acid modifications
	Modified residue	7	1	Phosphoserine By similarity
	Modified residue	21	1	Phosphothreonine By similarity
	Modified residue	22	1	Phosphoserine Ref.7
	Modified residue	204	1	N6-acetyllysine By similarity
	Modified residue	698	1	N6-acetyllysine By similarity
Experimental info
	Sequence conflict	319	1	H → R in BAE22102. Ref.1
	Sequence conflict	443	1	S → R in BAE22102. Ref.1
	Sequence conflict	453	1	L → I in BAE22102. Ref.1
	Sequence conflict	574	1	K → Q in BAE22102. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q3UYV9 [UniParc]. Last modified June 13, 2006. Version 2. Checksum: BE27F89BDBC19CF2	FASTA	790	91,927
	10 20 30 40 50 60 MSRRRHSYEN DGGQPHKRRK TSDANETEDH LESLICKVGE KSACSLESNL EGLAGVLEAD 70 80 90 100 110 120 LPNYKSKILR LLCTVARLLP EKLTIYTTLV GLLNARNYNF GGEFVEAMIR QLKESLKANN 130 140 150 160 170 180 YNEAVYLVRF LSDLVNCHVI AAPSMVAMFE NFVSVTQEED VPQVRRDWYV YAFLSSLPWV 190 200 210 220 230 240 GKELYEKKDA EMDRIFSTTE SYLKRRQKTH VPMLQVWTAD KPHPQEEYLD CLWAQIQKLK 250 260 270 280 290 300 KDRWQERHIL RPYLAFDSIL CEALQHNLPP FTPPPHTEDS VYPMPRVIFR MFDYTDDPEG 310 320 330 340 350 360 PVMPGSHSVE RFVIEENLHC IIKSYWKERK TCAAQLVSYP GKNKIPLNYH IVEVIFAELF 370 380 390 400 410 420 QLPAPPHIDV MYTTLLIELC KLQPGSLPQV LAQATEMLYM RLDTMSTTCV DRFINWFSHH 430 440 450 460 470 480 LSNFQFRWSW EDWSDCLTQD LESPKPKFVR EVLEKCMRLS YHQHILDIVP PTFSALCPAN 490 500 510 520 530 540 PTCIYKYGDE SSNSLPGHSV ALCLSVAFKS KATNDEIFSI LKDVPNPNQV DDDDEGFRFN 550 560 570 580 590 600 PLKIEVFVQT LLHLAAKSFS HSFSALAKFH EVFKTLAESD KGKLHVLRVM FEVWRNHPQM 610 620 630 640 650 660 IAVLVDKMIR TQIVDCAAVA NWIFSSELSR DFTRLFVWEI LHSTIRKMNK HVLKIQKELE 670 680 690 700 710 720 EAKEKLARQH KRRSDDDDRS SDRKDGALEE QIERLQEKVE AAQSEQKNLF LVIFQRFIMI 730 740 750 760 770 780 LTEHLVRCET DGTSILTPWY KNCIERLQQI FLQHHQTIQQ YMVTLENLLF TAELDPHILA 790 VFQQFCALQA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: C57BL/6J. Tissue: Testis and Thymus.
[2]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[3]	Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"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]. Strain: C57BL/6. Tissue: Brain.
[5]	"PHAX, a mediator of U snRNA nuclear export whose activity is regulated by phosphorylation." Ohno M., Segref A., Bachi A., Wilm M., Mattaj I.W. Cell 101:187-198(2000) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN A U SNRNA EXPORT COMPLEX WITH RNUXA/PHAX; NCBP2; RAN; XPO1 AND M7G-CAPPED RNA.
[6]	"The evolutionarily conserved region of the U snRNA export mediator PHAX is a novel RNA-binding domain that is essential for U snRNA export." Segref A., Mattaj I.W., Ohno M. RNA 7:351-360(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RNUXA/PHAX.
[7]	"Large-scale phosphorylation analysis of mouse liver." Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-22, MASS SPECTROMETRY. Tissue: Liver.
[8]	"Ars2 links the nuclear cap-binding complex to RNA interference and cell proliferation." Gruber J.J., Zatechka D.S., Sabin L.R., Yong J., Lum J.J., Kong M., Zong W.-X., Zhang Z., Lau C.-K., Rawlings J., Cherry S., Ihle J.N., Dreyfuss G., Thompson C.B. Cell 138:328-339(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN MIRNAS BIOGENESIS, INTERACTION WITH SRRT AND DROSHA.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AK134334 mRNA. Translation: BAE22102.1.
AK169557 mRNA. Translation: BAE41227.1.
AL929438, AL732615 Genomic DNA. Translation: CAM14995.1.
AL732615, AL929438 Genomic DNA. Translation: CAM17033.1.
CH466565 Genomic DNA. Translation: EDL02380.1.
BC055777 mRNA. Translation: AAH55777.1.
BC138898 mRNA. Translation: AAI38899.1.

IPI

IPI00458056.

RefSeq

NP_001028373.2. NM_001033201.3.

UniGene

Mm.389536.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3UKZ	X-ray	2.30	C	1-23	[»]
3UL0	X-ray	2.00	C	1-23	[»]

ProteinModelPortal

Q3UYV9.

SMR

Q3UYV9. Positions 2-790.

ModBase

Search...

PTM databases

PhosphoSite

Q3UYV9.

Proteomic databases

PaxDb

Q3UYV9.

PRIDE

Q3UYV9.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000030014; ENSMUSP00000030014; ENSMUSG00000028330.

GeneID

433702.

KEGG

mmu:433702.

UCSC

uc008stk.1. mouse.

Organism-specific databases

CTD

4686.

MGI

MGI:1891840. Ncbp1.

Phylogenomic databases

eggNOG

NOG303489.

GeneTree

ENSGT00390000001733.

HOGENOM

HOG000007990.

HOVERGEN

HBG080328.

InParanoid

B1AWH4.

KO

K12882.

OMA

LICRVGE.

OrthoDB

EOG4RXXZK.

Gene expression databases

Bgee

Q3UYV9.

Genevestigator

Q3UYV9.

GermOnline

ENSMUSG00000028330. Mus musculus.

Family and domain databases

Gene3D

1.25.40.180. 4 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

ChiTaRS

NCBP1. mouse.

NextBio

408905.

SOURCE

Search...

Entry information

Entry name

NCBP1_MOUSE

Accession

Primary (citable) accession number: Q3UYV9
Secondary accession number(s): B1AWH4, Q3TEM1, Q7TNE8

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 13, 2006
Last sequence update:	June 13, 2006
Last modified:	May 1, 2013
This is version 65 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program