8JJ2

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in one fab conformation

• PDB DOI: https://doi.org/10.2210/pdb8JJ2/pdb
• EM Map EMD-36338: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-05-29 Released: 2024-06-05 
• Deposition Author(s): Wang, H., Zhu, S.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab23

Wang, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 433.6 kDa 
• Atom Count: 26,196 
• Modelled Residue Count: 3,305 
• Deposited Residue Count: 3,863 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	A, C	841	Homo sapiens	Mutation(s): 0  Gene Names: GRIN2A, NMDAR2A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q12879 (Homo sapiens) Explore Q12879  Go to UniProtKB:  Q12879
PHAROS:  Q12879 GTEx:  ENSG00000183454

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	B, D	847	Homo sapiens	Mutation(s): 0  Gene Names: GRIN1, NMDAR1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens) Explore Q05586  Go to UniProtKB:  Q05586
PHAROS:  Q05586 GTEx:  ENSG00000176884

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab2G7 Heavy Chain	E	253	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab2G7 Light Chain	F	234	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth D], N [auth D], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Wang, H., Zhu, S.

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Funding Organization	Location	Grant Number
Other government	China	2022ZD0212700
Other government	China	LG 202106-02
Other government	China	2017YFA0505700
Other government	China	XDBS01020000
Other government	China	2018SHZDZX05

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release