5JTY

Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains with MPX-007


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors.

Yi, F.Mou, T.C.Dorsett, K.N.Volkmann, R.A.Menniti, F.S.Sprang, S.R.Hansen, K.B.

(2016) Neuron 91: 1316-1329

  • DOI: 10.1016/j.neuron.2016.08.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NMDA receptors mediate excitatory synaptic transmission and regulate synaptic plasticity in the central┬ánervous system, but their dysregulation is also implicated in numerous brain disorders. Here, we describe GluN2A-selective negative allosteric mod ...

    NMDA receptors mediate excitatory synaptic transmission and regulate synaptic plasticity in the central nervous system, but their dysregulation is also implicated in numerous brain disorders. Here, we describe GluN2A-selective negative allosteric modulators (NAMs) that inhibit NMDA receptors by stabilizing the apo state of the GluN1 ligand-binding domain (LBD), which is incapable of triggering channel gating. We describe structural determinants of NAM binding in crystal structures of the GluN1/2A LBD heterodimer, and analyses of NAM-bound LBD structures corresponding to active and inhibited receptor states reveal a molecular switch in the modulatory binding site that mediate the allosteric inhibition. NAM binding causes displacement of a valine in GluN2A and the resulting steric effects can be mitigated by the transition from glycine bound to apo state of the GluN1 LBD. This work provides mechanistic insight to allosteric NMDA receptor inhibition, thereby facilitating the development of novel classes NMDA receptor modulators as therapeutic agents.


    Organizational Affiliation

    Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1
A
292Rattus norvegicusMutation(s): 0 
Gene Names: Grin1 (Nmdar1)
Find proteins for P35439 (Rattus norvegicus)
Go to UniProtKB:  P35439
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
B
281Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
Find proteins for Q00959 (Rattus norvegicus)
Go to UniProtKB:  Q00959
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
B
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
6ND
Query on 6ND

Download SDF File 
Download CCD File 
B
5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide
C18 H17 F2 N5 O3 S2
GZXSPNTWOSSNMG-UHFFFAOYSA-N
 Ligand Interaction
2JK
Query on 2JK

Download SDF File 
Download CCD File 
A
4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid
C12 H11 N O3
JLHAMAZZACUPTQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.569α = 90.00
b = 89.684β = 90.00
c = 130.415γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references