Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.41 kDa 
• Atom Count: 4528 
• Residue Count: 547 
• Unique protein chains: 2

2A5T

Crystal Structure Of The NR1/NR2A ligand-binding cores complex

• DOI: 10.2210/pdb2A5T/pdb

• Classification: METAL TRANSPORT,MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus, Canis lupus familiaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-30 Released: 2005-11-15 
• Deposition Author(s): Furukawa, H., Singh, S.K., Mancusso, R., Gouaux, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

Literature

Subunit arrangement and function in NMDA receptors

Furukawa, H., Singh, S.K., Mancusso, R., Gouaux, E.

(2005) Nature 438: 185-192

• PubMed: 16281028 
• DOI: 10.1038/nature04089
• Primary Citation of Related Structures:  
  2A5T, 2A5S


• PubMed Abstract: 
  

Excitatory neurotransmission mediated by NMDA (N-methyl-D-aspartate) receptors is fundamental to the physiology of the mammalian central nervous system. These receptors are heteromeric ion channels that for activation require binding of glycine and glutamate to the NR1 and NR2 subunits, respectively. NMDA receptor function is characterized by slow channel opening and deactivation, and the resulting influx of cations initiates signal transduction cascades that are crucial to higher functions including learning and memory. Here we report crystal structures of the ligand-binding core of NR2A with glutamate and that of the NR1-NR2A heterodimer with glutamate and glycine. The NR2A-glutamate complex defines the determinants of glutamate and NMDA recognition, and the NR1-NR2A heterodimer suggests a mechanism for ligand-induced ion channel opening. Analysis of the heterodimer interface, together with biochemical and electrophysiological experiments, confirms that the NR1-NR2A heterodimer is the functional unit in tetrameric NMDA receptors and that tyrosine 535 of NR1, located in the subunit interface, modulates the rate of ion channel deactivation.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, New York 10032, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-methyl-D-aspartate receptor NMDAR1-4a subunit	A	292	Rattus norvegicus, Canis lupus familiaris This entity is chimeric	Mutation(s): 0  Gene Names: Grin1
Find proteins for P35439 (Rattus norvegicus) Explore P35439  Go to UniProtKB:  P35439

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-methyl-D-aspartate receptor NMDAR2A subunit	B	284	Rattus norvegicus	Mutation(s): 0  Gene Names: Grin2a
Find proteins for Q00959 (Rattus norvegicus) Explore Q00959  Go to UniProtKB:  Q00959

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU	B	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
GLY	A	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GGL	EC50:  1000   nM  BindingDB
GGL	Ki:  100   nM  BindingDB
GGL	Ki:  1600   nM  BindingDB
GGL	EC50:  2900   nM  BindingDB
GLY	IC50:  250   nM  BindingDB
GLY	IC50:  6200   nM  BindingDB
GGL	EC50:  5750   nM  BindingDB
GGL	EC50:  450   nM  BindingDB
GGL	EC50:  1800   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.64	α = 90
b = 89.989	β = 90
c = 126.116	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-30 
• Released Date: 2005-11-15 
Deposition Author(s): Furukawa, H., Singh, S.K., Mancusso, R., Gouaux, E.

Revision History 

• Version 1.0: 2005-11-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-26
  Changes: Refinement description, Source and taxonomy