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Protein

Nuclear cap-binding protein subunit 1

Gene

Ncbp1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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. Associates with NCBP3 to form an alternative cap-binding complex (CBC) which plays a key role in mRNA export and is particularly important in cellular stress situations such as virus infections. The conventional CBC with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus whereas the alternative CBC with NCBP3 does not bind snRNA and associates only with mRNA thereby playing a role only in mRNA export. NCBP1/CBP80 is required for cell growth and viability (By similarity).By similarity

GO - Molecular functioni

  • mRNA binding Source: GO_Central
  • RNA 7-methylguanosine cap binding Source: RGD
  • RNA cap binding Source: GO_Central

GO - Biological processi

Keywordsi

Biological processmRNA capping, mRNA processing, mRNA splicing, mRNA transport, Nonsense-mediated mRNA decay, RNA-mediated gene silencing, Translation regulation, Transport

Enzyme and pathway databases

ReactomeiR-RNO-109688 Cleavage of Growing Transcript in the Termination Region
R-RNO-111367 SLBP independent Processing of Histone Pre-mRNAs
R-RNO-112382 Formation of RNA Pol II elongation complex
R-RNO-113418 Formation of the Early Elongation Complex
R-RNO-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-RNO-191859 snRNP Assembly
R-RNO-674695 RNA Polymerase II Pre-transcription Events
R-RNO-6803529 FGFR2 alternative splicing
R-RNO-6807505 RNA polymerase II transcribes snRNA genes
R-RNO-72086 mRNA Capping
R-RNO-72163 mRNA Splicing - Major Pathway
R-RNO-72165 mRNA Splicing - Minor Pathway
R-RNO-72187 mRNA 3'-end processing
R-RNO-72203 Processing of Capped Intron-Containing Pre-mRNA
R-RNO-77588 SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
R-RNO-77595 Processing of Intronless Pre-mRNAs
R-RNO-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

Names & Taxonomyi

Protein namesi
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 namesi
Name:Ncbp1
Synonyms:Cbp80
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 5

Organism-specific databases

RGDi1308973 Ncbp1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002397801 – 790Nuclear cap-binding protein subunit 1Add BLAST790

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei7PhosphoserineCombined sources1
Modified residuei21PhosphothreonineBy similarity1
Modified residuei22PhosphoserineBy similarity1
Modified residuei201PhosphoserineBy similarity1
Modified residuei204N6-acetyllysineBy similarity1
Cross-linki684Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei698N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ56A27
PRIDEiQ56A27

PTM databases

iPTMnetiQ56A27
PhosphoSitePlusiQ56A27

Expressioni

Gene expression databases

BgeeiENSRNOG00000023605
GenevisibleiQ56A27 RN

Interactioni

Subunit structurei

Component of the nuclear cap-binding complex (CBC), a heterodimer composed of NCBP1/CBP80 and NCBP2/CBP20 that interacts with m7GpppG-capped RNA. Found in a U snRNA export complex containing PHAX/RNUXA, NCBP1/CBP80, NCBP2/CBP20, RAN, XPO1 and m7G-capped RNA. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with PHAX/RNUXA, SRRT/ARS2, EIF4G2, IGF2BP1, HNRNPF, HNRNPH1, KIAA0427/CTIF, PARN, DROSHA, UPF1 and ALYREF/THOC4. May interact with EIF4G1; the interaction is however controversial since it is reported by, and, but is not observed by. The large PER complex involved in the repression of transcriptional termination is composed of at least PER2, CDK9, DDX5, DHX9, NCBP1/CBP80 and POLR2A. Component of an alternative nuclear cap-binding complex (CBC) composed of NCBP1/CBP80 and NCBP3. Interacts with METTL3. Interacts with ZFC3H1 in a RNase-insensitive manner (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000038713

Structurei

3D structure databases

ProteinModelPortaliQ56A27
SMRiQ56A27
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini28 – 240MIF4GAdd BLAST213

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili643 – 713Sequence analysisAdd BLAST71

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi3 – 20Nuclear localization signalSequence analysisAdd BLAST18

Sequence similaritiesi

Belongs to the NCBP1 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG1104 Eukaryota
ENOG410XR7H LUCA
GeneTreeiENSGT00390000001733
HOGENOMiHOG000007990
HOVERGENiHBG080328
InParanoidiQ56A27
KOiK12882
OMAiLICRVGE
OrthoDBiEOG091G02OT
PhylomeDBiQ56A27
TreeFamiTF313400

Family and domain databases

Gene3Di1.25.40.180, 4 hits
InterProiView protein in InterPro
IPR016024 ARM-type_fold
IPR027159 CBP80
IPR016021 MIF4-like_sf
IPR015172 MIF4G-like_typ-1
IPR015174 MIF4G-like_typ-2
IPR003890 MIF4G-like_typ-3
PANTHERiPTHR12412 PTHR12412, 1 hit
PfamiView protein in Pfam
PF02854 MIF4G, 1 hit
PF09088 MIF4G_like, 1 hit
PF09090 MIF4G_like_2, 1 hit
SMARTiView protein in SMART
SM00543 MIF4G, 1 hit
SUPFAMiSSF48371 SSF48371, 3 hits

Sequencei

Sequence statusi: Complete.

Q56A27-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRRRHSYEN DGGQPHKRRK TSDANETEDH LESLICKVGE KSACSLESNL
60 70 80 90 100
EGLAGVLEAD LPNYKSKILR LLCTVARLLP EKLTIYTTLV GLLNARNYNF
110 120 130 140 150
GGEFVEAMIR QLKESLKANN YNEAVYLVRF LSDLVNCHVI AAPSMVAMFE
160 170 180 190 200
NFVSVTQEED VPQVRRDWYV YAFLSSLPWV GKELYEKKDA EMDRIFSSTE
210 220 230 240 250
SYLKRRQKTH VPMLQVWTAD KPHPQEEYLD CLWAQIQKLK KDRWQERHIL
260 270 280 290 300
RPYLAFDSIL CEALQHNLPP FTPPPHTEDS VYPMPRVIFR MFDYTDDPEG
310 320 330 340 350
PVMPGSHSVE RFVIEENLHC IIKSYWKERK TCAAQLVSYP GKNKIPLNYH
360 370 380 390 400
IVEVIFAELF QLPAPPHIDV MYTTLLIELC KLQPGSLPQV LAQATEMLYM
410 420 430 440 450
RLDTMSTTCV DRFINWFSHH LSNFQFRWSW EDWSDCLTQD LESPKPKFVR
460 470 480 490 500
EVLEKCMRLS YHQHILDIVP PTFSALCPAN PTCIYKYGDE SSNSLPGHSV
510 520 530 540 550
ALCLSVAFKS KATNDEIFSI LKDVPNPNQV DDDDEGFRFN PLKIEVFVQT
560 570 580 590 600
LLHLAAKSFS HSFSALAKFH EVFKTLAESD KGKLHVLRVM FEVWRNHPQM
610 620 630 640 650
IAVLVDKMIR TQIVDCAAVA NWIFSSELSR DFTRLFVWEI LHSTIRKMNK
660 670 680 690 700
HVLKIQKELE EAKEKLARQH KRRSDDDDRG SDRKDGALEE QIERLQEKVE
710 720 730 740 750
SAQSEQKNLF LVIFQRFIMI LTEHLVRCET DGTSILTPWY KNCIERLQQI
760 770 780 790
FLQHHQIIQQ YMVTLENLLF TAELDPHILA VFQQFCALQA
Length:790
Mass (Da):91,911
Last modified:May 10, 2005 - v1
Checksum:iD50595780E7FCDBF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC092199 mRNA Translation: AAH92199.1
RefSeqiNP_001014785.1, NM_001014785.1
UniGeneiRn.13482

Genome annotation databases

EnsembliENSRNOT00000030825; ENSRNOP00000038713; ENSRNOG00000023605
GeneIDi298075
KEGGirno:298075
UCSCiRGD:1308973 rat

Similar proteinsi

Entry informationi

Entry nameiNCBP1_RAT
AccessioniPrimary (citable) accession number: Q56A27
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 13, 2006
Last sequence update: May 10, 2005
Last modified: May 23, 2018
This is version 108 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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