5IOU

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine-bound conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of NMDA Receptor Inhibition and Activation.

Zhu, S.Stein, R.A.Yoshioka, C.Lee, C.H.Goehring, A.Mchaourab, H.S.Gouaux, E.

(2016) Cell 165: 704-714

  • DOI: https://doi.org/10.1016/j.cell.2016.03.028
  • Primary Citation of Related Structures:  
    5IOU, 5IOV, 5IPQ, 5IPR, 5IPS, 5IPT, 5IPU, 5IPV

  • PubMed Abstract: 

    N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated, calcium-permeable ion channels that mediate synaptic transmission and underpin learning and memory. NMDAR dysfunction is directly implicated in diseases ranging from seizure to ischemia. Despite its fundamental importance, little is known about how the NMDAR transitions between inactive and active states and how small molecules inhibit or activate ion channel gating. Here, we report electron cryo-microscopy structures of the GluN1-GluN2B NMDA receptor in an ensemble of competitive antagonist-bound states, an agonist-bound form, and a state bound with agonists and the allosteric inhibitor Ro25-6981. Together with double electron-electron resonance experiments, we show how competitive antagonists rupture the ligand binding domain (LBD) gating "ring," how agonists retain the ring in a dimer-of-dimers configuration, and how allosteric inhibitors, acting within the amino terminal domain, further stabilize the LBD layer. These studies illuminate how the LBD gating ring is fundamental to signal transduction and gating in NMDARs.


  • Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-methyl-D-aspartate receptor subunit NR1-8aA,
B [auth C]
822Xenopus laevisMutation(s): 14 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Explore A0A1L8F5J9 
Go to UniProtKB:  A0A1L8F5J9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L8F5J9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ionotropic glutamate receptor subunit NR2BC [auth B],
D
825Xenopus laevisMutation(s): 10 
Gene Names: NR2B
Membrane Entity: Yes 
UniProt
Find proteins for A7XY94 (Xenopus laevis)
Explore A7XY94 
Go to UniProtKB:  A7XY94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7XY94
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references