Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0005948
UniProt IDQ09161
Primary gene name(s)NCBP1
Synonym gene name(s)CBP80, NCBP
Protein nameNuclear cap-binding protein subunit 1
Protein functionComponent 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, PubMed:26382858. {ECO:0000269|PubMed:11551508, ECO:0000269|PubMed:12093754, ECO:0000269|PubMed:15059963, ECO:0000269|PubMed:15361857, ECO:0000269|PubMed:16186820, ECO:0000269|PubMed:16317009, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:17873884, ECO:0000269|PubMed:18369367, ECO:0000269|PubMed:19632182, ECO:0000269|PubMed:19648179, ECO:0000269|PubMed:26382858, ECO:0000269|PubMed:7651522, ECO:0000269|PubMed:8069914}.
Subcellular locationNucleus {ECO:0000269|PubMed:19648179}. Cytoplasm {ECO:0000269|PubMed:17289661}. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. {ECO:0000269|PubMed:17289661}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q09161
Gene Ontology
(Biological Process)
Complete annatation
7-methylguanosine mRNA capping [GO:0006370];
fibroblast growth factor receptor signaling pathway [GO:0008543];
gene expression [GO:0010467];
gene silencing by RNA [GO:0031047];
histone mRNA metabolic process [GO:0008334];
mRNA 3'-end processing [GO:0031124];
mRNA cis splicing, via spliceosome [GO:0045292];
mRNA export from nucleus [GO:0006406];
mRNA splicing, via spliceosome [GO:0000398];
nuclear export [GO:0051168];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
positive regulation of cell growth [GO:0030307];
positive regulation of mRNA 3'-end processing [GO:0031442];
pre-mRNA cleavage required for polyadenylation [GO:0098789];
regulation of translational initiation [GO:0006446];
RNA export from nucleus [GO:0006405];
RNA splicing [GO:0008380];
snRNA transcription from RNA polymerase II promoter [GO:0042795];
termination of RNA polymerase II transcription [GO:0006369];
transcription elongation from RNA polymerase II promoter [GO:0006368];
transcription from RNA polymerase II promoter [GO:0006366]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723];
RNA cap binding [GO:0000339]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytosol [GO:0005829];
intracellular ribonucleoprotein complex [GO:0030529];
mitochondrion [GO:0005739];
mRNA cap binding complex [GO:0005845];
nuclear cap binding complex [GO:0005846];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
RNA cap binding complex [GO:0034518]
Protein-protein interaction110766
Phylogenetic treeQ09161
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD30.7455443477999880.02402191550845690.0542003458897399
AZA vs. DISU-0.09496810404335850.707423750333990.972282962725769
AZA vs. IL70.2094292432468270.2766712637079020.999311006273513
AZA vs. SAHA0.1012390709003690.6789603726729680.906362792921743
DISU vs. CD3-0.8529686488708080.02001695480113830.0514121976204687
DISU vs. IL70.2955826071984470.2411739378985960.625980908027089
DISU vs. SAHA0.1967225974881550.5001691644128410.825168632531976
DMSO vs. AZA-0.0004878368408963020.9976814582381971
DMSO vs. CD3-0.7581062461299780.01874152407878840.0423808256149725
DMSO vs. DISU0.09244806000381620.7048571375329890.96015520768527
DMSO vs. IL70.2172571552774460.2275929722268790.735469251086859
DMSO vs. SAHA0.09454042314780020.6892750778605270.904208912309365
HIV vs. Mock in Activation-0.09407676993961610.8798563882468910.999983755607037
HIV vs. Mock in Latency-0.0384369804552630.8162070080071580.999834320637052
IL7 vs. CD3-0.5273765914654060.1021542189934490.193026268382632
SAHA vs. CD3-0.6697276315249150.06229924017348150.119052694574482
SAHA vs. IL7-0.1123759149655130.645718044054960.825814643865345
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) unknown
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.0763825 0.740718
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
1.044 1.034 1.063 1.032 1.107
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
209520_s_at 1.69 No upregulated in CD8+ cells

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1H2T X-ray 2.1Å C=20-652# C=702-790.
1H2U X-ray 2.4Å A/B=20-652# A/B=702-790.
1H2V X-ray 2.0Å C=20-790.
1H6K X-ray 2.0Å A/B/C=20-790.
1N52 X-ray 2.1Å A=1-790.
1N54 X-ray 2.7Å A=1-790.
3FEX X-ray 3.5Å A=1-790.
3FEY X-ray 2.2Å A=1-790.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03013 RNA transport - Homo sapiens (human)
hsa03015 mRNA surveillance pathway - Homo sapiens (human)
hsa03040 Spliceosome - Homo sapiens (human)