9C7R | pdb_00009c7r

Diheteromeric GluN1/GluN2A (M817V) in digitonin complexed with glycine, glutamate, and GNE-4123

PDB DOI: https://doi.org/10.2210/pdb9C7R/pdb
EM Map EMD-45285: EMDB EMDataResource

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

Deposited: 2024-06-11 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: 3.99 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 (M817V), in complex with glycine, glutamate, and GNE-4123

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

To be published.

Macromolecule Content

Total Structure Weight: 514.24 kDa
Atom Count: 25,867
Modeled Residue Count: 3,173
Deposited Residue Count: 4,470
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
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P35439-1
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	1,127	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
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain B Focus chain D	Go to GlyGen: Q00959-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, I E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth B] DA [auth B] EA [auth B] AA [auth A], BA [auth A], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth D], KA [auth D], LA [auth D], MA [auth D], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain Y [auth A] Focus chain Z [auth A]