4NF5

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and D-AP5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.903 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into Competitive Antagonism in NMDA Receptors.

Jespersen, A.Tajima, N.Fernandez-Cuervo, G.Garnier-Amblard, E.C.Furukawa, H.

(2014) Neuron 81: 366-378

  • DOI: 10.1016/j.neuron.2013.11.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There has been a great level of enthusiasm to downregulate overactive N-methyl-D-aspartate (NMDA) receptors to protect neurons from excitotoxicity. NMDA receptors play pivotal roles in basic brain development and functions as well as in neurological ...

    There has been a great level of enthusiasm to downregulate overactive N-methyl-D-aspartate (NMDA) receptors to protect neurons from excitotoxicity. NMDA receptors play pivotal roles in basic brain development and functions as well as in neurological disorders and diseases. However, mechanistic understanding of antagonism in NMDA receptors is limited due to complete lack of antagonist-bound structures for the L-glutamate-binding GluN2 subunits. Here, we report the crystal structures of GluN1/GluN2A NMDA receptor ligand-binding domain (LBD) heterodimers in complex with GluN1- and GluN2-targeting antagonists. The crystal structures reveal that the antagonists, D-(-)-2-amino-5-phosphonopentanoic acid (D-AP5) and 1-(phenanthrene-2-carbonyl)piperazine-2,3-dicarboxylic acid (PPDA), have discrete binding modes and mechanisms for opening of the bilobed architecture of GluN2A LBD compared to the agonist-bound form. The current study shows distinct ways by which the conformations of NMDA receptor LBDs may be controlled and coupled to receptor inhibition and provides possible strategies to develop therapeutic compounds with higher subtype-specificity.


    Organizational Affiliation

    Cold Spring Harbor Laboratory, WM Keck Structural Biology Laboratory, 1 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
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
B
283Rattus norvegicusMutation(s): 1 
Gene Names: Grin2a
Find proteins for Q00959 (Rattus norvegicus)
Go to UniProtKB:  Q00959
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2JJ
Query on 2JJ

Download SDF File 
Download CCD File 
B
5-phosphono-D-norvaline
C5 H12 N O5 P
VOROEQBFPPIACJ-SCSAIBSYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.903 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.029α = 90.00
b = 87.344β = 90.00
c = 121.269γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Advisory, Refinement description, Source and taxonomy