9PZT | pdb_00009pzt

Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state

• PDB DOI: https://doi.org/10.2210/pdb9PZT/pdb
• EM Map EMD-72080: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-08-11 Released: 2025-12-17 
• Deposition Author(s): Kim, J., 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: 6.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state

Kim, J., Gouaux, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E2F2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A8B2C2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 714.46 kDa 
• Atom Count: 24,381 
• Modeled Residue Count: 3,446 
• Deposited Residue Count: 6,390 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2	A [auth L], G [auth J]	141	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2	B [auth M], H [auth K]	131	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	C [auth D], I [auth B]	1,464	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P35436 (Mus musculus) Explore P35436  Go to UniProtKB:  P35436

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	D [auth C], J [auth A]	938	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P35438 (Mus musculus) Explore P35438  Go to UniProtKB:  P35438
IMPC:  MGI:95819

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11	E [auth H], K [auth F]	277	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11	F [auth I], L [auth G]	244	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth E]	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.14 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., 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