Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 84.97 kDa 
• Atom Count: 5023 
• Modelled Residue Count: 706 
• Deposited Residue Count: 745 
• Unique protein chains: 2

5TPZ

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in apo closed state

• PDB DOI: 10.2210/pdb5TPZ/pdb

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


• Deposited: 2016-10-21 Released: 2016-12-14 
• Deposition Author(s): Romero-Hernandez, A., Simorwski, N., Karakas, E., Furukawa, H.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.300 
• R-Value Work: 0.240 
• R-Value Observed: 0.244 

Literature

Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain.

Romero-Hernandez, A., Simorowski, N., Karakas, E., Furukawa, H.

(2016) Neuron 92: 1324-1336

• PubMed: 27916457 
• DOI: 10.1016/j.neuron.2016.11.006
• Primary Citation of Related Structures:  
  5TPW, 5TPZ, 5TQ0, 5TQ2


• PubMed Abstract: 
  

Zinc is vastly present in the mammalian brain and controls functions of various cell surface receptors to regulate neurotransmission. A distinctive characteristic of N-methyl-D-aspartate (NMDA) receptors containing a GluN2A subunit is that their ion channel activity is allosterically inhibited by a nano-molar concentration of zinc that binds to an extracellular domain called an amino-terminal domain (ATD). Despite physiological importance, the molecular mechanism underlying the high-affinity zinc inhibition has been incomplete because of the lack of a GluN2A ATD structure. Here we show the first crystal structures of the heterodimeric GluN1-GluN2A ATD, which provide the complete map of the high-affinity zinc-binding site and reveal distinctive features from the ATD of the GluN1-GluN2B subtype. Perturbation of hydrogen bond networks at the hinge of the GluN2A bi-lobe structure affects both zinc inhibition and open probability, supporting the general model in which the bi-lobe motion in ATD regulates the channel activity in NMDA receptors.

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Organizational Affiliation: 

WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NMDA glutamate receptor subunit	A	383	Xenopus laevis	Mutation(s): 2  Gene Names: grin1, NR1
UniProt
Find proteins for A0A1L8F5J9 (Xenopus laevis) Explore A0A1L8F5J9  Go to UniProtKB:  A0A1L8F5J9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2B	B [auth D]	362	Rattus norvegicus	Mutation(s): 1  Gene Names: Grin2b
UniProt
Find proteins for Q00960 (Rattus norvegicus) Explore Q00960  Go to UniProtKB:  Q00960

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.300 
• R-Value Work: 0.240 
• R-Value Observed: 0.244 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.782	α = 90
b = 75.782	β = 90
c = 548.556	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-21 
• Released Date: 2016-12-14 
Deposition Author(s): Romero-Hernandez, A., Simorwski, N., Karakas, E., Furukawa, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	MH085926
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM1055730

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2018-05-16
  Changes: Data collection, Database references
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence, Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary