9OBW | pdb_00009obw

Mg2+ bound GluN1a/2B NMDAR (lower)

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Rattus norvegicus
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2025-04-23 Released: 2026-05-06 
  • Deposition Author(s): Steigerwald, R., Furukawa, H.
  • Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9OBW

This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism of calcium permeability and magnesium block in NMDA receptors.

Steigerwald, R.Epstein, M.Chou, T.H.Simorowski, N.Furukawa, H.

(2026) Nat Neurosci 

  • DOI: https://doi.org/10.1038/s41593-026-02283-3
  • Primary Citation Related Structures: 
    9OBS, 9OBT, 9OBU, 9OBV, 9OBW, 9OBX, 9OBY, 9OBZ, 9OC0, 9OC1, 9OC2

  • PubMed Abstract: 

    Hebbian neuroplasticity, which is thought to be a cellular substrate of learning and memory, can occur by means of coincidental detection of presynaptic neurotransmitter release and Ca 2+ influx upon postsynaptic depolarization. This is mediated at a molecular level by N-methyl-D-aspartate-type glutamate receptors, which bind glutamate and glycine and facilitate Ca 2+ influx upon relief of Mg 2+ channel block during membrane depolarization. However, the structural mechanism underlying Ca 2+ permeability and Mg 2+ blockade in N-methyl-D-aspartate-type glutamate receptors has yet to be fully elucidated. Here we demonstrate using single-particle cryo-electron microscopy that Ca 2+ permeation through the narrow constriction of the cation selectivity filter involves partial dehydration, as evidenced by several Ca 2+ binding sites. In contrast, Mg 2+ binds outside of the selectivity filter through a water network and remains hydrated, thereby acting as a channel blocker. Furthermore, the lipid network around the selectivity filter influences the stability of Mg 2+ binding in a voltage-dependent manner. Our study details the transmembrane chemistry essential for initiating neuroplasticity.


  • Organizational Affiliation
    • W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 386.51 kDa 
  • Atom Count: 3,762 
  • Modeled Residue Count: 500 
  • Deposited Residue Count: 3,418 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1
A, C
847Rattus norvegicusMutation(s): 0 
Gene Names: Grin1Nmdar1
UniProt
Find proteins for P35439 (Rattus norvegicus)
Explore P35439 
Go to UniProtKB:  P35439
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2B
B, D
862Rattus norvegicusMutation(s): 0 
Gene Names: Grin2b
UniProt
Find proteins for Q00960 (Rattus norvegicus)
Explore Q00960 
Go to UniProtKB:  Q00960
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00960
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH085926
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS111745

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Data collection, Database references