9PZS | pdb_00009pzs

Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate bound state

• PDB DOI: https://doi.org/10.2210/pdb9PZS/pdb
• EM Map EMD-72078: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda, Homo sapiens
• 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: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate-bound state

Kim, J., Gouaux, E.

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 - A6B2C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 688.51 kDa 
• Atom Count: 24,307 
• Modeled Residue Count: 3,413 
• Deposited Residue Count: 6,136 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2B	A [auth D]	1,482	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q01097 (Mus musculus) Explore Q01097  Go to UniProtKB:  Q01097
IMPC:  MGI:95821
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q01097-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	B [auth A], F [auth C]	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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P35438-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11	C [auth F], I [auth H]	277	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11	D [auth G], J [auth I]	244	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	E [auth B]	1,464	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P35436 (Mus musculus) Explore P35436  Go to UniProtKB:  P35436

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2	G [auth J]	141	Mus musculus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2	H [auth K]	131	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth E], L, N, O, P	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	Q [auth A], R [auth B], S [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 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