4PE5

Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Rattus norvegicus
  • Expression System: Spodoptera frugiperda
  • Mutation(s): 22 

  • Deposited: 2014-04-22 Released: 2014-06-04 
  • Deposition Author(s): Karakas, E., Furukawa, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute of Mental Health; Robertson Research Fund; Mirus Research Award 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of a heterotetrameric NMDA receptor ion channel.

Karakas, E.Furukawa, H.

(2014) Science 344: 992-997

  • DOI: 10.1126/science.1251915

  • PubMed Abstract: 
  • N-Methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event f ...

    N-Methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event for initiation of neuronal plasticity. Here, we show the crystal structure of the intact heterotetrameric GluN1-GluN2B NMDA receptor ion channel at 4 angstroms. The NMDA receptors are arranged as a dimer of GluN1-GluN2B heterodimers with the twofold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD), and a transmembrane domain (TMD). The ATD and LBD are much more highly packed in the NMDA receptors than non-NMDA receptors, which may explain why ATD regulates ion channel activity in NMDA receptors but not in non-NMDA receptors.


    Organizational Affiliation

    Cold Spring Harbor Laboratory, W. M. Keck Structural Biology Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 1
A, C
825Rattus norvegicusMutation(s): 15 
Gene Names: Grin1 (Nmdar1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluN1a/GluN2B NMDA receptor
Find proteins for P35439 (Rattus norvegicus)
Go to UniProtKB:  P35439
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2B
B, D
820Rattus norvegicusMutation(s): 7 
Gene Names: Grin2b
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluN1a/GluN2B NMDA receptor
Find proteins for Q00960 (Rattus norvegicus)
Go to UniProtKB:  Q00960
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
A, C
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
QEL
Query on QEL

Download SDF File 
Download CCD File 
B, C
4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol
C21 H27 N O2
UYNVMODNBIQBMV-KKSFZXQISA-N
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
B, D
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
W
Query on W

Download SDF File 
Download CCD File 
A, B, C
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QELKi: 10 - 29 nM (97) BINDINGDB
QELKd: 94 nM (97) BINDINGDB
QELIC50: 20 - 110 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.256 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 116.825α = 90.00
b = 163.186β = 93.81
c = 163.137γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM105730
National Institutes of Health/National Institute of Mental HealthUnited StatesMH085926
Robertson Research FundUnited States--
Mirus Research AwardUnited States--

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-06-11
    Type: Database references
  • Version 1.2: 2014-07-30
    Type: Derived calculations
  • Version 2.0: 2017-09-06
    Type: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary