9D3C | pdb_00009d3c

Gly-,Glu-,(S)-(+)-ketamine bound GluN1a-2B-2D NMDAR

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): Yes 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2024-08-09 Released: 2025-02-26 
  • Deposition Author(s): Hyunook, K., Hiro, F.
  • 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: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9D3C

This is version 1.2 of the entry. See complete history

Literature

Structural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor.

Kang, H.Epstein, M.Banke, T.G.Perszyk, R.Simorowski, N.Paladugu, S.Liotta, D.C.Traynelis, S.F.Furukawa, H.

(2025) Neuron 113: 991

  • DOI: https://doi.org/10.1016/j.neuron.2025.01.013
  • Primary Citation Related Structures: 
    9D37, 9D38, 9D39, 9D3A, 9D3B, 9D3C

  • PubMed Abstract: 

    Discrete activation of N-methyl-D-aspartate receptor (NMDAR) subtypes by glutamate and the co-agonist glycine is fundamental to neuroplasticity. A distinct variant, the tri-heteromeric receptor, comprising glycine-binding GluN1 and two types of glutamate-binding GluN2 subunits, exhibits unique pharmacological characteristics, notably enhanced sensitivity to the anti-depressant channel blocker S-(+)-ketamine. Despite its significance, the structural mechanisms underlying ligand gating and channel blockade of tri-heteromeric NMDARs remain poorly understood. Here, we identify and characterize tri-heteromeric GluN1-2B-2D NMDAR in the adult brain, resolving its structures in the activated, inhibited, and S-(+)-ketamine-blocked states. These structures reveal the ligand-dependent conformational dynamics that modulate the tension between the extracellular domain and transmembrane channels, governing channel gating and blockade. Additionally, we demonstrate that the inhibitor (S)-DQP-997-74 selectively decouples linker tension in GluN2D, offering insights into subtype-selective targeting for cognitive modulation.


  • Organizational Affiliation
    • W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Macromolecule Content 

  • Total Structure Weight: 381 kDa 
  • Atom Count: 24,194 
  • Modeled Residue Count: 3,115 
  • Deposited Residue Count: 3,395 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1
A, C
825Homo sapiensMutation(s): 3 
Gene Names: GRIN1NMDAR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens)
Explore Q05586 
Go to UniProtKB:  Q05586
PHAROS:  Q05586
GTEx:  ENSG00000176884 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05586
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q05586-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2B884Homo sapiensMutation(s): 3 
Gene Names: GRIN2BNMDAR2B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13224 (Homo sapiens)
Explore Q13224 
Go to UniProtKB:  Q13224
PHAROS:  Q13224
GTEx:  ENSG00000273079 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13224
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q13224-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2D861Homo sapiensMutation(s): 0 
Gene Names: GRIN2DGluN2DNMDAR2D
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O15399 (Homo sapiens)
Explore O15399 
Go to UniProtKB:  O15399
PHAROS:  O15399
GTEx:  ENSG00000105464 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15399
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O15399-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JC9
(Subject of Investigation/LOI)

Query on JC9



Download:Ideal Coordinates CCD File
M [auth B](2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
C13 H16 Cl N O
YQEZLKZALYSWHR-ZDUSSCGKSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
O [auth C],
P [auth C],
Q [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLU
(Subject of Investigation/LOI)

Query on GLU



Download:Ideal Coordinates CCD File
K [auth B],
R [auth D]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
GLY
(Subject of Investigation/LOI)

Query on GLY



Download:Ideal Coordinates CCD File
F [auth A],
N [auth C]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
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: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-16
    Changes: Data collection, Database references