Tbio NCBP2 Nuclear cap-binding protein subunit 2

Protein Classes

PANTHER Classes

Protein / Nucleic Acid Binding / Rna Binding Protein / Nuclear Cap-binding Protein Subunit 2

DTO Classes

Protein / Nucleic Acid Binding / Rna Binding Protein / Nuclear Cap-binding Protein Subunit 2

Protein Summary

Description

Component 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). The product of this gene is a component of the nuclear cap-binding protein complex (CBC), which binds to the monomethylated 5' cap of nascent pre-mRNA in the nucleoplasm. The encoded protein has an RNP domain commonly found in RNA binding proteins, and contains the cap-binding activity. The CBC promotes pre-mRNA splicing, 3'-end processing, RNA nuclear export, and nonsense-mediated mRNA decay. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• P52298
• B2RE91
• B4DMK7
• E9PAR5
• Q14924
• Q2TS50

Gene Name

• NCBP2

Ensembl ID

• ENST00000321256
• ENSP00000326806
• ENSG00000114503
• ENST00000427641
• ENSP00000397619
• ENST00000452404
• ENSP00000412785

Symbol

• CBP20
• CBC2
• NIP1
• CBP20
• PIG55

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological process	0.94
transcription factor binding site profile	0.89
histone modification site profile	0.86
hub protein	0.75
pathway	0.68

Related Tools

Target Illumination GWAS Analytics (TIGA)

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GENEVA

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 67.69   (req: < 5)

Gene RIFs: 7   (req: <= 3)

Antibodies: 162   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 67.69   (req: >= 5)

Gene RIFs: 7   (req: > 3)

Antibodies: 162   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 27

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

GWAS Traits (2)

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GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
HIV-1 infection	EFO_0000180	1	1	1		61.5
viral load	EFO_0010125	1	1	1		61.5

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
HIV-1 infection	EFO_0000180	1		61.5
viral load	EFO_0010125	1		61.5

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Orthologs (14)

1 – 5 of 14

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Macaque	nuclear cap binding protein subunit 2		708260
Mouse	nuclear cap binding protein subunit 2	MGI:1915342	68092
Rat	nuclear cap binding protein subunit 2	RGD:1596188	689116
Dog	nuclear cap binding protein subunit 2	VGNC:43646	478603
Horse	nuclear cap binding protein subunit 2	VGNC:20582	100060150

Species	Name	OMA	EggNOG	Inparanoid
Macaque	nuclear cap binding protein subunit 2
Mouse	nuclear cap binding protein subunit 2
Rat	nuclear cap binding protein subunit 2
Dog	nuclear cap binding protein subunit 2
Horse	nuclear cap binding protein subunit 2

Protein Structure (11 Structures, 1 AlphaFold Model)

Representation

  axes   backbone   ball+stick   cartoon   rocket   rope   spacefill

Color Scheme

  target   atomindex   bfactor   chainname   electrostatic   element   hydrophobicity   resname   sstruc

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-P52298-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 11

PDB Structure Id	Ligand	Method	Resolution (Å)	Residues	Fraction of Total Protein	Pub Year	Title

PDB Structure Id	Fraction of Total Protein	Resolution	Pub Year

Pathways (60)

Reactome (56)

KEGG (3)

WikiPathways (1)

Abortive elongation of HIV-1 transcript in the absence of Tat (R-HSA-167242)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Abortive elongation of HIV-1 transcript in the absence of Tat	23 targets	R-HSA-167242
Reactome	Axon guidance	533 targets	R-HSA-422475
Reactome	Developmental Biology	1055 targets	R-HSA-1266738
Reactome	Disease	1105 targets	R-HSA-1643685
Reactome	Diseases of signal transduction	387 targets	R-HSA-5663202

Name	Explore in Pharos	Explore in Source
Abortive elongation of HIV-1 transcript in the absence of Tat	23 targets	R-HSA-167242
Axon guidance	533 targets	R-HSA-422475
Developmental Biology	1055 targets	R-HSA-1266738
Disease	1105 targets	R-HSA-1643685
Diseases of signal transduction	387 targets	R-HSA-5663202

Gene Ontology Terms (34)

Functions (5)

Components (7)

Processes (22)

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10

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GO Term	Evidence	Assigned by
mRNA binding	Inferred from Direct Assay (IDA)	UniProtKB
RNA 7-methylguanosine cap binding	Inferred from Direct Assay (IDA)	UniProtKB
snRNA binding	Inferred from Direct Assay (IDA)	UniProtKB
RNA binding	Inferred from High Throughput Direct Assay (HDA)	UniProtKB
RNA cap binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central

Protein-Protein Interactions (571)

Explore Interacting Targets

1 – 10 of 571

• See Interactions on String-DB

SMG1

Tchem

Family: Kinase

Novelty: 0.00854339

Score: 0.999

Data Source: STRINGDB

RBM8A

Tbio

Novelty: 0.00052175

Score: 0.999

Data Source: STRINGDB

NCBP1

Tbio

Novelty: 0.01228885

Score: 0.999

Data Source: Reactome,STRINGDB

DDIT4L

Tbio

Novelty: 0.08748295

Score: 0.993

Data Source: STRINGDB

PHAX

Tbio

Novelty: 0.04027466

Score: 0.991

Data Source: Reactome,STRINGDB

SRRT

Tbio

Novelty: 0.00429818

Score: 0.99

Data Source: Reactome,STRINGDB

MTREX

Tbio

Novelty: 0.01358024

Score: 0.987

Data Source: STRINGDB

UPF1

Tbio

Novelty: 0.00311006

Score: 0.987

Data Source: STRINGDB

EIF4G1

Tbio

Novelty: 0.00170995

Score: 0.986

Data Source: Reactome,STRINGDB

SF3A2

Tbio

Novelty: 0.03658692

Score: 0.986

Data Source: STRINGDB

Publication Statistics

PubMed Score  67.69

PubMed score by year

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PubTator Score  28.75

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

3D-structure
Acetylation
Alternative splicing
Complete proteome
Cytoplasm
Direct protein sequencing
Methylation
mRNA processing
mRNA splicing
mRNA transport

GWAS Trait Find Similar Targets

HIV-1 infection
viral load

MGI Phenotype Find Similar Targets

behavior/neurological phenotype
homeostasis/metabolism phenotype
mortality/aging