9C7P | pdb_00009c7p

Diheteromeric GluN1/GluN2A (delM653) in digitonin complexed with glycine, glutamate, and GNE-4123

• PDB DOI: https://doi.org/10.2210/pdb9C7P/pdb
• EM Map EMD-45283: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus, Aequorea victoria
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-06-10 Released: 2025-09-24 
• Deposition Author(s): Jalali-Yazdi, F., Kim, J., Gouaux, E.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Diheteromeric NMDA receptor GluN1/GluN2A, in complex with glycine, glutamate, and GNE-4123

Jalali-Yazdi, F., Kim, J., Gouaux, E.

To be published.

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: electron microscopy

Macromolecule Content 

• Total Structure Weight: 502.23 kDa 
• Atom Count: 25,132 
• Modeled Residue Count: 3,178 
• Deposited Residue Count: 4,468 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1, Green fluorescent protein chimera	A, C	1,108	Rattus norvegicus, Aequorea victoria This entity is chimeric	Mutation(s): 0  Gene Names: Grin1, Nmdar1, GFP
UniProt
Find proteins for P35439 (Rattus norvegicus) Explore P35439  Go to UniProtKB:  P35439
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
UniProt Groups	P42212P35439

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A, Green fluorescent protein chimera	B, D	1,126	Rattus norvegicus, Aequorea victoria This entity is chimeric	Mutation(s): 0  Gene Names: Grin2a, GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for Q00959 (Rattus norvegicus) Explore Q00959  Go to UniProtKB:  Q00959
UniProt Groups	Q00959P42212

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Jalali-Yazdi, F., Kim, J., Gouaux, E.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	--

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release