5JTY | pdb_00005jty

Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains with MPX-007

• PDB DOI: https://doi.org/10.2210/pdb5JTY/pdb

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


• Deposited: 2016-05-10 Released: 2016-09-21 
• Deposition Author(s): Mou, T.-C., Sprang, S.R., Hansen, K.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.278 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors.

Yi, F., Mou, T.C., Dorsett, K.N., Volkmann, R.A., Menniti, F.S., Sprang, S.R., Hansen, K.B.

(2016) Neuron 91: 1316-1329

• PubMed: 27618671 
• DOI: https://doi.org/10.1016/j.neuron.2016.08.014
• Primary Citation Related Structures: 
  5I56, 5I57, 5I58, 5I59, 5JTY


• PubMed Abstract: 
  

  NMDA receptors mediate excitatory synaptic transmission and regulate synaptic plasticity in the central nervous system, but their dysregulation is also implicated in numerous brain disorders. Here, we describe GluN2A-selective negative allosteric modulators (NAMs) that inhibit NMDA receptors by stabilizing the apo state of the GluN1 ligand-binding domain (LBD), which is incapable of triggering channel gating. We describe structural determinants of NAM binding in crystal structures of the GluN1/2A LBD heterodimer, and analyses of NAM-bound LBD structures corresponding to active and inhibited receptor states reveal a molecular switch in the modulatory binding site that mediate the allosteric inhibition. NAM binding causes displacement of a valine in GluN2A and the resulting steric effects can be mitigated by the transition from glycine bound to apo state of the GluN1 LBD. This work provides mechanistic insight to allosteric NMDA receptor inhibition, thereby facilitating the development of novel classes NMDA receptor modulators as therapeutic agents.

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Organizational Affiliation: 
• Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812, USA.
Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
BioPharmaWorks, LLC, Groton, CT 06340, USA.
MindImmune Therapeutics, Inc., and George & Anne Ryan Institute for Neuroscience, Kingston, RI 02881, USA.
Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812, USA; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 65.69 kDa 
• Atom Count: 4,434 
• Modeled Residue Count: 538 
• Deposited Residue Count: 573 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1	A	292	Rattus norvegicus	Mutation(s): 0  Gene Names: Grin1, Nmdar1
UniProt
Find proteins for P35439 (Rattus norvegicus) Explore P35439  Go to UniProtKB:  P35439

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A	B	281	Rattus norvegicus	Mutation(s): 0  Gene Names: Grin2a
UniProt
Find proteins for Q00959 (Rattus norvegicus) Explore Q00959  Go to UniProtKB:  Q00959

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ND	D [auth B]	5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide C18 H17 F2 N5 O3 S2 GZXSPNTWOSSNMG-UHFFFAOYSA-N
2JK	C [auth A]	4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid C12 H11 N O3 JLHAMAZZACUPTQ-UHFFFAOYSA-N
GLU	E [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6ND	BindingDB:  5JTY	IC50: 16.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.278 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.569	α = 90
b = 89.684	β = 90
c = 130.415	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Mou, T.-C., Sprang, S.R., Hansen, K.B.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-10-05
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary