8JF7 | pdb_00008jf7

Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab

• PDB DOI: https://doi.org/10.2210/pdb8JF7/pdb
• EM Map EMD-36209: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus, Muromegalovirus G4, Mus musculus
• Expression System: Homo sapiens, Mus musculus
• Mutation(s): No 


• Deposited: 2023-05-17 Released: 2024-05-22 
• Deposition Author(s): Kou, Z., Zhu, S.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Probing the architecture of native GluN1-N2-N3A NMDA receptors by cryo-EM and click chemistry.

Kou, Z., Zhu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A4B2C2D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 599.95 kDa 
• Atom Count: 31,416 
• Modeled Residue Count: 4,009 
• Deposited Residue Count: 5,385 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	A, C	847	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,Enhanced green fluorescent protein	B	1,116	Rattus norvegicus, Muromegalovirus G4 This entity is chimeric	Mutation(s): 0  Gene Names: Grin2a, eGFP
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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 3A,Enhanced green fluorescent protein	D	1,228	Rattus norvegicus, Muromegalovirus G4 This entity is chimeric	Mutation(s): 0  Gene Names: Grin3a, eGFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for Q9R1M7 (Rattus norvegicus) Explore Q9R1M7  Go to UniProtKB:  Q9R1M7
UniProt Groups	P42212Q9R1M7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GluN1-specific antibody fragment light chain	E, G	237	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
GluN1-specific antibody fragment heavy chain	F, H	217	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
GluN2A-specific antibody fragment light chain	I [auth K]	212	Mus musculus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
GluN2A-specific antibody fragment heavy chain	J	227	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Kou, Z., Zhu, S.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-23
  Changes: Data collection