Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 376.30 kDa 
• Atom Count: 15321 
• Modelled Residue Count: 3105 
• Deposited Residue Count: 3346 
• Unique protein chains: 2

5FXJ

GluN1b-GluN2B NMDA receptor structure-Class X

• PDB DOI: 10.2210/pdb5FXJ/pdb
• EM Map EMD-3355: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-03-02 Released: 2016-05-25 
• Deposition Author(s): Tajima, N., Karakas, E., Grant, T., Simorowski, N., Diaz-Avalos, R., Grigorieff, N., Furukawa H, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Activation of Nmda Receptors and the Mechanism of Inhibition by Ifenprodil.

Tajima, N., Karakas, E., Grant, T., Simorowski, N., Diaz-Avalos, R., Grigorieff, N., Furukawa, H.

(2016) Nature 534: 63

• PubMed: 27135925 
• DOI: 10.1038/nature17679
• Primary Citation of Related Structures:  
  5B3J, 5FXG, 5FXH, 5FXI, 5FXJ, 5FXK


• PubMed Abstract: 
  

The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino-terminal domain (ATD). Recent crystal structures of GluN1-GluN2B NMDA receptors bound to agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here we applied X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology to rat NMDA receptors to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open conformation accompanied by rearrangement of the GluN1-GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel.

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Organizational Affiliation: 

Cold Spring Harbor Laboratory, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York 11724, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1	A, C	846	Rattus norvegicus	Mutation(s): 14  Gene Names: Grin1, Nmdar1 Membrane Entity: Yes
UniProt
Find proteins for P35439 (Rattus norvegicus) Explore P35439  Go to UniProtKB:  P35439

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2B	B, D	827	Rattus norvegicus	Mutation(s): 5  Gene Names: Grin2b Membrane Entity: Yes
UniProt
Find proteins for Q00960 (Rattus norvegicus) Explore Q00960  Go to UniProtKB:  Q00960

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-02 
• Released Date: 2016-05-25 
Deposition Author(s): Tajima, N., Karakas, E., Grant, T., Simorowski, N., Diaz-Avalos, R., Grigorieff, N., Furukawa H, H.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references