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GRIN2B glutamate ionotropic receptor NMDA type subunit 2B [ Homo sapiens (human) ]

Gene ID: 2904, updated on 1-Jun-2020

Summary

Official Symbol
GRIN2Bprovided by HGNC
Official Full Name
glutamate ionotropic receptor NMDA type subunit 2Bprovided by HGNC
Primary source
HGNC:HGNC:4586
See related
Ensembl:ENSG00000273079 MIM:138252
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NR3; MRD6; NR2B; hNR3; EIEE27; GluN2B; NMDAR2B
Summary
This gene encodes a member of the N-methyl-D-aspartate (NMDA) receptor family within the ionotropic glutamate receptor superfamily. The encoded protein is a subunit of the NMDA receptor ion channel which acts as an agonist binding site for glutamate. The NMDA receptors mediate a slow calcium-permeable component of excitatory synaptic transmission in the central nervous system. The NMDA receptors are heterotetramers of seven genetically encoded, differentially expressed subunits including NR1 (GRIN1), NR2 (GRIN2A, GRIN2B, GRIN2C, or GRIN2D) and NR3 (GRIN3A or GRIN3B). The early expression of this gene in development suggests a role in brain development, circuit formation, synaptic plasticity, and cellular migration and differentiation. Naturally occurring mutations within this gene are associated with neurodevelopmental disorders including autism spectrum disorder, attention deficit hyperactivity disorder, epilepsy, and schizophrenia. [provided by RefSeq, Aug 2017]
Expression
Biased expression in brain (RPKM 5.9) and testis (RPKM 0.2) See more
Orthologs

Genomic context

See GRIN2B in Genome Data Viewer
Location:
12p13.1
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (13537337..13982012, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (13713684..14133022, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 590, pseudogene Neighboring gene Sharpr-MPRA regulatory region 1480 Neighboring gene uncharacterized LOC105369668 Neighboring gene RN7SK pseudogene 162 Neighboring gene uncharacterized LOC105369667 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 23 Neighboring gene MRPS18C pseudogene 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2019-09-25)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2019-09-25)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study of aging.
NHGRI GWA Catalog
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
NHGRI GWA Catalog
Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
NHGRI GWA Catalog
Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women.
NHGRI GWA Catalog
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
NHGRI GWA Catalog
Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of glutamate receptor, ionotropic, N-methyl D-aspartate 2B (GRIN2B) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 induced-neurotoxicity involves upregulation of NR2B and downregulation of PSD-95 expressions in neuron cells PubMed
env HIV-1 gp120-induced dephosphorylation of KV2.1 is dependent on NMDA receptor-mediated activation of protein phosphatase 2B or calcineurin PubMed
env HIV-1 gp120 activates forward trafficking and surface clustering of NMDA receptors in membrane microdomains by a PKA-dependent phosphorylation of the NR1 C-terminal Ser897, followed by a PKC-dependent phosphorylation of Ser896 PubMed
env HIV-1 gp120-induced synapse loss requires sequential activation of CXCR4, IL-1beta receptor, and NMDA receptor PubMed
env HIV-1 gp120 activates NMDA receptor directly and phosphorylates JNK through a gp120-mediated apoptotic pathway in human neuroblastoma cells PubMed
env HIV-1 clade B gp120 significantly downregulates NMDA receptor gene and protein expression and levels of glutamine compared to clade C gp120 PubMed
env HIV-1 gp120-mediated human cell death involves the NMDA receptor complex; antagonists of the NMDA receptor reverse the gp120-mediated effects PubMed
env HIV-1 gp120 causes an activation of phospholipase A2, resulting in the increased release of arachidonic acid, which may sensitize the NMDA receptor PubMed
env HIV-1 gp120 binds to cells expressing epsilon1/zeta1 or epsilon2/zeta1 combined NMDA receptor subunits, but not to cells expressing a single epsilon1, epsilon2, or zeta1 NMDA receptor subunit PubMed
Tat tat The gene expression of GRIN2B is significantly upregulated in both clade B and clade C Tat treated SK-N-MC neuroblastoma cells PubMed
tat Ca(2+) influx through the NMDA receptor is necessary for HIV-1 Tat-induced synapse loss PubMed
tat HIV-1 Tat upregulates the expression of NMDARs for the apoptosis of retinal pigmen epithelium (RPE) cells. Silencing of NMDARs by siRNA abolishes Tat-induced RPE apoptosis PubMed
tat HIV-1 Tat-induced activation of spermine oxidase (SMO) activity involves NMDAR stimulation in human neuroblastoma PubMed
tat HIV-1 Tat-induced loss of presynaptic terminals is recovered by ifenprodil, an NR2B subunit-selective NMDA receptor antagonist PubMed
tat HIV-1 Tat and methamphetamine inhibit the normal conjunction of signaling between D1 and NMDA receptors, resulting in neural dysfunction and death PubMed
tat HIV-1 Tat interacts with NMDA receptors in primary neuronal-glial cultures and in hippocampal slice cultures PubMed
tat Tat treatment causes activation of neuronal nitric oxide synthase (nNOS) through association with NMDA receptors PubMed
tat HIV-1 Tat treatment induces the formation of complexes involving the low-density lipoprotein receptor-related protein (LRP), postsynaptic density protein-95 (PSD-95), and N-methyl-d-aspartic acid (NMDA) receptors at the neuron surface PubMed
tat HIV-1 Tat-induced NMDA receptor activation is clade dependent. The Cys 30-Cys 31 motif in Tat is critical for the NMDA receptor activation PubMed
tat HIV-1 Tat induces apoptosis of neurons and neurotoxicity through the activation of both NMDA and non-NMDA receptors PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC142178, MGC142180

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NMDA glutamate receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NMDA glutamate receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
NMDA glutamate receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
NMDA glutamate receptor activity TAS
Traceable Author Statement
more info
PubMed 
amyloid-beta binding NAS
Non-traceable Author Statement
more info
PubMed 
glutamate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
glutamate receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glutamate-gated calcium ion channel activity IDA
Inferred from Direct Assay
more info
PubMed 
glutamate-gated calcium ion channel activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
glycine binding IDA
Inferred from Direct Assay
more info
PubMed 
ligand-gated ion channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
MAPK cascade TAS
Traceable Author Statement
more info
 
brain development NAS
Non-traceable Author Statement
more info
PubMed 
calcium ion transmembrane import into cytosol IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion transmembrane import into cytosol IMP
Inferred from Mutant Phenotype
more info
PubMed 
calcium-mediated signaling IEA
Inferred from Electronic Annotation
more info
 
chemical synaptic transmission TAS
Traceable Author Statement
more info
PubMed 
ephrin receptor signaling pathway TAS
Traceable Author Statement
more info
 
excitatory chemical synaptic transmission NAS
Non-traceable Author Statement
more info
PubMed 
excitatory postsynaptic potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glutamate receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
ionotropic glutamate receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
learning or memory ISS
Inferred from Sequence or Structural Similarity
more info
 
long-term synaptic potentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
modulation of chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
multicellular organism development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of dendritic spine maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cysteine-type endopeptidase activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of neuron death ISS
Inferred from Sequence or Structural Similarity
more info
 
protein heterotetramerization ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of NMDA receptor activity TAS
Traceable Author Statement
more info
 
regulation of synaptic plasticity NAS
Non-traceable Author Statement
more info
PubMed 
response to ethanol IDA
Inferred from Direct Assay
more info
PubMed 
synaptic transmission, glutamatergic IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
NMDA selective glutamate receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NMDA selective glutamate receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
NMDA selective glutamate receptor complex TAS
Traceable Author Statement
more info
PubMed 
cell IEA
Inferred from Electronic Annotation
more info
 
cell surface ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
late endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
lysosome ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic membrane TAS
Traceable Author Statement
more info
PubMed 
synaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
glutamate receptor ionotropic, NMDA 2B
Names
N-methyl D-aspartate receptor subtype 2B
N-methyl-D-aspartate receptor subunit 3
glutamate [NMDA] receptor subunit epsilon-2
glutamate receptor subunit epsilon-2
glutamate receptor, ionotropic, N-methyl D-aspartate 2B

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031854.2 RefSeqGene

    Range
    6657..449676
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000834.5NP_000825.2  glutamate receptor ionotropic, NMDA 2B precursor

    See identical proteins and their annotated locations for NP_000825.2

    Status: REVIEWED

    Source sequence(s)
    AC007527, AC007535, AC007916, U88963, U90278
    Consensus CDS
    CCDS8662.1
    UniProtKB/Swiss-Prot
    Q13224
    Conserved Domains (5) summary
    cd06378
    Location:33393
    PBP1_iGluR_NMDA_NR2; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family
    COG0834
    Location:459542
    HisJ; ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]
    cd13718
    Location:403803
    PBP2_iGluR_NMDA_Nr2; The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily
    pfam00060
    Location:557829
    Lig_chan; Ligand-gated ion channel
    pfam10565
    Location:8401484
    NMDAR2_C; N-methyl D-aspartate receptor 2B3 C-terminus

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    13537337..13982012 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520629.2XP_011518931.1  glutamate receptor ionotropic, NMDA 2B isoform X1

    See identical proteins and their annotated locations for XP_011518931.1

    UniProtKB/Swiss-Prot
    Q13224
    Conserved Domains (5) summary
    cd06378
    Location:33393
    PBP1_iGluR_NMDA_NR2; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family
    COG0834
    Location:459542
    HisJ; ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]
    cd13718
    Location:403803
    PBP2_iGluR_NMDA_Nr2; The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily
    pfam00060
    Location:557829
    Lig_chan; Ligand-gated ion channel
    pfam10565
    Location:8401484
    NMDAR2_C; N-methyl D-aspartate receptor 2B3 C-terminus
  2. XM_017019219.2XP_016874708.1  glutamate receptor ionotropic, NMDA 2B isoform X1

    UniProtKB/Swiss-Prot
    Q13224
    Related
    ENSP00000477455.1, ENST00000609686.3
    Conserved Domains (5) summary
    cd06378
    Location:33393
    PBP1_iGluR_NMDA_NR2; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family
    COG0834
    Location:459542
    HisJ; ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]
    cd13718
    Location:403803
    PBP2_iGluR_NMDA_Nr2; The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily
    pfam00060
    Location:557829
    Lig_chan; Ligand-gated ion channel
    pfam10565
    Location:8401484
    NMDAR2_C; N-methyl D-aspartate receptor 2B3 C-terminus
  3. XM_005253351.3XP_005253408.1  glutamate receptor ionotropic, NMDA 2B isoform X2

    Conserved Domains (2) summary
    pfam10565
    Location:102746
    NMDAR2_C; N-methyl D-aspartate receptor 2B3 C-terminus
    cl21456
    Location:165
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
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