5FXG

GLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE CONFORMATION


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1038/nature17679
  • Primary Citation of Related Structures:  

  • 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 NM ...

    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.


    Organizational Affiliation

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA.,Cold Spring Harbor Laboratory, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York 11724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-METHYL-D-ASPARTATE RECEPTOR GLUN1
A, C
846Rattus norvegicusMutation(s): 14 
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
N-METHYL-D-ASPARTATE RECEPTOR GLUN2B
B, D
827Rattus norvegicusMutation(s): 5 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2017-04-19
    Type: Other
  • Version 1.3: 2017-08-23
    Type: Data collection