Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0005949
UniProt IDP52298
Primary gene name(s)NCBP2
Synonym gene name(s)CBP20
Protein nameNuclear cap-binding protein subunit 2
Protein functionComponent of the cap-binding complex, CBC, which binds co-transcriptionally 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, thereby being 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, NCBP2/CBP20 recognizes and binds capped RNAs, m7GpppG-capped RNA but requires NCBP1/CBP80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. The conventional cap-binding complex with NCBP2 binds both small nuclear RNA, snRNA and messenger, mRNA and is involved in their export from the nucleus, PubMed:26382858. {ECO:0000269|PubMed:11551508, ECO:0000269|PubMed:15361857, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:17363367, ECO:0000269|PubMed:17873884, ECO:0000269|PubMed:18369367, ECO:0000269|PubMed:19632182, ECO:0000269|PubMed:26382858}.
Subcellular locationNucleus {ECO:0000269|PubMed:8601613}. Cytoplasm {ECO:0000269|PubMed:8601613}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P52298
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 mRNA 3'-end processing [GO:0031442];
positive regulation of RNA export from nucleus [GO:0046833];
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 export from nucleus [GO:0006408];
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
mRNA binding [GO:0003729];
nucleotide binding [GO:0000166];
poly(A RNA binding [GO:0044822];
RNA 7-methylguanosine cap binding [GO:0000340];
RNA cap binding [GO:0000339];
snRNA binding [GO:0017069]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytosol [GO:0005829];
mRNA cap binding complex [GO:0005845];
nuclear cap binding complex [GO:0005846];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction116578
Phylogenetic treeP52298
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      unknown
Interferon-stimulated
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. CD31.27282240779130.0001291770101558010.000606528316843686
AZA vs. DISU-0.02581696211315430.9186332231601510.994399291201374
AZA vs. IL70.1614338962841340.4008882224433880.999311006273513
AZA vs. SAHA-0.3371719886584040.1682547373759920.523158397525929
DISU vs. CD3-1.311520325203120.0003722668985917110.00177132298906927
DISU vs. IL70.1783296384767830.4787051159388350.81294126650647
DISU vs. SAHA-0.3101679283809890.2882267075595410.671074418295975
DMSO vs. AZA-0.06074336133773180.7168789850384791
DMSO vs. CD3-1.343869464728433.60961938098425e-050.00018132349441323
DMSO vs. DISU-0.03646710111317890.8810848532114560.987443803738299
DMSO vs. IL70.2293059134113990.2021761064068840.712770066436806
DMSO vs. SAHA-0.28363473474150.2301747414972730.576780776685216
HIV vs. Mock in Activation-0.09764831290458040.8751102024972380.999983755607037
HIV vs. Mock in Latency-0.001757585770977120.9914950750894470.999834320637052
IL7 vs. CD3-1.103332626239750.0006839132665029670.00306530617484366
SAHA vs. CD3-1.634778496481737.15639729986783e-064.70126012680943e-05
SAHA vs. IL7-0.5021372463458830.04011347308003550.157930171420495
(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 -0.139225 0.371203
(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
1.017 0.837 0.929 0.964 0.952
(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
unknown unknown unknown unknown

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 Z=1-156.
1H2U X-ray 2.4Å X/Y=1-156.
1H2V X-ray 2.0Å Z=1-156.
1H6K X-ray 2.0Å X/Y/Z=22-120.
1N52 X-ray 2.1Å B=1-156.
1N54 X-ray 2.7Å B=1-156.
3FEX X-ray 3.5Å B=1-156.
3FEY X-ray 2.2Å B=1-156.

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)
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