9C7E | pdb_00009c7e

Diheteromeric GluN1/GluN2A (delM653) in nanodisc complex with glycine, glutamate, and GNE-4123, open conformation, C2 symmetry

PDB DOI: https://doi.org/10.2210/pdb9C7E/pdb
EM Map EMD-45279: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Rattus norvegicus, Aequorea victoria
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-06-10 Released: 2025-09-24
Deposition Author(s): Jalali-Yazdi, F., Kim, J., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Diheteromeric GluN1/GluN2A (delM653) in nanodisc complexed with glycine, glutamate, and GNE-4123, open-pore conformation, processed in C2 symmetry

Jalali-Yazdi, F., Kim, J., Gouaux, E.

To be published.

Macromolecule Content

Total Structure Weight: 506.35 kDa
Atom Count: 25,434
Modeled Residue Count: 3,178
Deposited Residue Count: 4,468
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1,Green fluorescent protein chimera	A, C	1,108	Rattus norvegicus, Aequorea victoria This entity is chimeric	Mutation(s): 0 Gene Names: Grin1, Nmdar1, GFP
UniProt
Find proteins for P35439 (Rattus norvegicus) Explore P35439 Go to UniProtKB: P35439
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P42212P35439
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera	B, D	1,126	Rattus norvegicus, Aequorea victoria This entity is chimeric	Mutation(s): 0 Gene Names: Grin2a, GFP
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q00959P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 (Subject of Investigation/LOI) Query on Y01 Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain I [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain N [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain N [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B] G [auth B] I [auth B] K [auth D] L [auth D] F [auth B], G [auth B], I [auth B], K [auth D], L [auth D], N [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth D]
A1AUV (Subject of Investigation/LOI) Query on A1AUV Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth C]	4-cyclohexyl-N-[(8R)-2-cyclopropyl-7-hydroxy-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]benzene-1-sulfonamide C₂₁ H₂₅ N₅ O₃ S NVBBYGHRHGFNKE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain H [auth B]	H [auth B], M [auth D]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain M [auth D]