3OEK | pdb_00003oek

Crystal structure of GluN2D ligand-binding core in complex with L-aspartate

• PDB DOI: https://doi.org/10.2210/pdb3OEK/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-12 Released: 2011-05-11 
• Deposition Author(s): Simorowski, N., Furukawa, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptors.

Vance, K.M., Simorowski, N., Traynelis, S.F., Furukawa, H.

(2011) Nat Commun 2: 294-294

• PubMed: 21522138 
• DOI: https://doi.org/10.1038/ncomms1295
• Primary Citation Related Structures: 
  3OEK, 3OEL, 3OEM, 3OEN


• PubMed Abstract: 
  

  N-methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors that mediate a majority of excitatory synaptic transmission. One unique property of GluN1/GluN2D NMDA receptors is an unusually prolonged deactivation time course following the removal of L-glutamate. Here we show, using x-ray crystallography and electrophysiology, that the deactivation time course of GluN1/GluN2D receptors is influenced by the conformational variability of the ligand-binding domain (LBD) as well as the structure of the activating ligand. L-glutamate and L-CCG-IV induce significantly slower deactivation time courses compared with other agonists. Crystal structures of the isolated GluN2D LBD in complex with various ligands reveal that the binding of L-glutamate induces a unique conformation at the backside of the ligand-binding site in proximity to the region at which the transmembrane domain would be located in the intact receptors. These data suggest that the activity of the GluN1/GluN2D NMDA receptor is controlled distinctively by the endogenous neurotransmitter L-glutamate.

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Organizational Affiliation: 
• Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, Georgia 30322-3090, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.17 kDa 
• Atom Count: 2,381 
• Modeled Residue Count: 270 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate [NMDA] receptor subunit epsilon-4	A	286	Rattus norvegicus	Mutation(s): 0  Gene Names: GluN2D, Grin2d
UniProt
Find proteins for Q62645 (Rattus norvegicus) Explore Q62645  Go to UniProtKB:  Q62645

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP	B [auth A]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.728	α = 90
b = 114.062	β = 90
c = 94.928	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Simorowski, N., Furukawa, H.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-23
  Changes: Source and taxonomy
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary