9PZQ | pdb_00009pzq

GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 1), glycine- and glutamate-bound state

• PDB DOI: https://doi.org/10.2210/pdb9PZQ/pdb
• EM Map EMD-72076: EMDB EMDataResource

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


• Deposited: 2025-08-11 Released: 2025-12-17 
• Deposition Author(s): Kim, J., Jalali-Yazdi, F., Gouaux, E.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.07 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 1), glycine- and glutamate-bound state

Kim, J., Jalali-Yazdi, F., Gouaux, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 426.64 kDa 
• Atom Count: 21,983 
• Modeled Residue Count: 3,010 
• Deposited Residue Count: 3,914 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polyclonal antibody Fab fragment, termed FabEnc1	A [auth F], B [auth G]	244	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	C [auth A], E [auth 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	D [auth B], F [auth D]	866	Rattus norvegicus	Mutation(s): 0  Gene Names: Grin2a
UniProt
Find proteins for Q00959 (Rattus norvegicus) Explore Q00959  Go to UniProtKB:  Q00959

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.07 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.
RECONSTRUCTION	cryoSPARC	4.4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Kim, J., Jalali-Yazdi, F., 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	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release