3JPY

Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit NR2B

• PDB DOI: https://doi.org/10.2210/pdb3JPY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2009-09-04 Released: 2009-12-08 
• Deposition Author(s): Karakas, E., Simorowski, N., Furukawa, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 0.233 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit.

Karakas, E., Simorowski, N., Furukawa, H.

(2009) EMBO J 28: 3910-3920

• PubMed: 19910922 
• DOI: https://doi.org/10.1038/emboj.2009.338
• Primary Citation of Related Structures:  
  3JPW, 3JPY


• PubMed Abstract: 
  

  N-methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors (iGluRs) that mediate the majority of fast excitatory synaptic transmission in the mammalian brain. One of the hallmarks for the function of NMDA receptors is that their ion channel activity is allosterically regulated by binding of modulator compounds to the extracellular amino-terminal domain (ATD) distinct from the L-glutamate-binding domain. The molecular basis for the ATD-mediated allosteric regulation has been enigmatic because of a complete lack of structural information on NMDA receptor ATDs. Here, we report the crystal structures of ATD from the NR2B NMDA receptor subunit in the zinc-free and zinc-bound states. The structures reveal the overall clamshell-like architecture distinct from the non-NMDA receptor ATDs and molecular determinants for the zinc-binding site, ion-binding sites, and the architecture of the putative phenylethanolamine-binding site.

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Organizational Affiliation: 

WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.25 kDa 
• Atom Count: 2,651 
• Modelled Residue Count: 358 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate [NMDA] receptor subunit epsilon-2	A	363	Rattus norvegicus	Mutation(s): 1  Gene Names: Grin2b
UniProt
Find proteins for Q00960 (Rattus norvegicus) Explore Q00960  Go to UniProtKB:  Q00960
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q00960-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 0.233 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.368	α = 90
b = 143.368	β = 90
c = 88.467	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Karakas, E., Simorowski, N., Furukawa, H.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.3: 2021-10-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description