6MMB | pdb_00006mmb

Diheteromeric NMDA receptor GluN1/GluN2A in the 'Super-Splayed' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1

• PDB DOI: https://doi.org/10.2210/pdb6MMB/pdb
• EM Map EMD-9149: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-09-30 Released: 2018-11-28 
• Deposition Author(s): Jalali-Yazdi, F., Chowdhury, S., Yoshioka, C., Gouaux, E.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 12.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor.

Jalali-Yazdi, F., Chowdhury, S., Yoshioka, C., Gouaux, E.

(2018) Cell 175: 1520-1532.e15

• PubMed: 30500536 
• DOI: https://doi.org/10.1016/j.cell.2018.10.043
• Primary Citation Related Structures: 
  6MM9, 6MMA, 6MMB, 6MMG, 6MMH, 6MMI, 6MMJ, 6MMK, 6MML, 6MMM, 6MMN, 6MMP, 6MMR, 6MMS, 6MMT, 6MMU, 6MMV, 6MMW, 6MMX


• PubMed Abstract: 
  

  N-methyl-D-aspartate receptors (NMDARs) play essential roles in memory formation, neuronal plasticity, and brain development, with their dysfunction linked to a range of disorders from ischemia to schizophrenia. Zinc and pH are physiological allosteric modulators of NMDARs, with GluN2A-containing receptors inhibited by nanomolar concentrations of divalent zinc and by excursions to low pH. Despite the widespread importance of zinc and proton modulation of NMDARs, the molecular mechanism by which these ions modulate receptor activity has proven elusive. Here, we use cryoelectron microscopy to elucidate the structure of the GluN1/GluN2A NMDAR in a large ensemble of conformations under a range of physiologically relevant zinc and proton concentrations. We show how zinc binding to the amino terminal domain elicits structural changes that are transduced though the ligand-binding domain and result in constriction of the ion channel gate.

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Organizational Affiliation: 
• Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA.
Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA; Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR 97239, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 383.38 kDa 
• Atom Count: 24,494 
• Modeled Residue Count: 3,039 
• Deposited Residue Count: 3,350 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	A, C	838	Rattus norvegicus	Mutation(s): 0  Gene Names: Grin1, Nmdar1 Membrane Entity: Yes
UniProt
Find proteins for P35439 (Rattus norvegicus) Explore P35439  Go to UniProtKB:  P35439
Glycosylation
Glycosylation Sites: 11		Go to GlyGen: P35439-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	B, D	837	Rattus norvegicus	Mutation(s): 0  Gene Names: Grin2a Membrane Entity: Yes
UniProt
Find proteins for Q00959 (Rattus norvegicus) Explore Q00959  Go to UniProtKB:  Q00959
Glycosylation
Glycosylation Sites: 6		Go to GlyGen: Q00959-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], N [auth A], O [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 12.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	cisTEM

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Jalali-Yazdi, F., Chowdhury, S., Yoshioka, C., Gouaux, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS038631
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	1F32MH115595

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Refinement description, Structure summary