9C7C | pdb_00009c7c

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

PDB DOI: https://doi.org/10.2210/pdb9C7C/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: 3.10 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 (delM563) in nanodisc, in complex with glycine, glutamate, and GNE-4123, open-pore conformation

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

To be published.

Macromolecule Content

Total Structure Weight: 518.21 kDa
Atom Count: 26,221
Modeled Residue Count: 3,180
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	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: 11	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	1,126	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
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	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 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
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 9 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 BB [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain IA [auth B] SDF format, chain TA [auth C] SDF format, chain Y [auth A] SDF format, chain CB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain CB [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain CB [auth D]	BB [auth D] CB [auth D] FA [auth B] FB [auth D] GA [auth B] BB [auth D], CB [auth D], FA [auth B], FB [auth D], GA [auth B], IA [auth B], TA [auth C], Y [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain BB [auth D] Focus chain CB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain TA [auth C] Focus chain Y [auth A] Interactions & Density Focus chain BB [auth D] Focus chain CB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain TA [auth C] Focus chain Y [auth A]
A1AUV Query on A1AUV Download Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain P [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain P [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain P [auth A]	LA [auth C], P [auth A]	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 LA [auth C] Focus chain P [auth A] Interactions & Density Focus chain LA [auth C] Focus chain P [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth D] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] SDF format, chain XA [auth D] SDF format, chain S [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain S [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain S [auth A]	AA [auth B] AB [auth D] BA [auth B] CA [auth B] DA [auth B] AA [auth B], AB [auth D], BA [auth B], CA [auth B], DA [auth B], EA [auth B], MA [auth C], NA [auth C], OA [auth C], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], T [auth A], U [auth A], V [auth A], VA [auth D], W [auth A], WA [auth D], XA [auth D], YA [auth D], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain HA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain HA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain HA [auth B]	DB [auth D], HA [auth B]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain DB [auth D] Focus chain HA [auth B] Interactions & Density Focus chain DB [auth D] Focus chain HA [auth B]
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain GB [auth D] SDF format, chain JA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain JA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain JA [auth B]	GB [auth D], JA [auth B]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain GB [auth D] Focus chain JA [auth B] Interactions & Density Focus chain GB [auth D] Focus chain JA [auth B]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain SA [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain SA [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain SA [auth C]	KA [auth B], SA [auth C]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Focus chain SA [auth C] Interactions & Density Focus chain KA [auth B] Focus chain SA [auth C]
HP6 Query on HP6 Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain EB [auth D] MOL2 format, chain EB [auth D] mmCIF format, chain EB [auth D]	EB [auth D]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain EB [auth D] Interactions & Density Focus chain EB [auth D]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain UA [auth C] SDF format, chain Z [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain Z [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain Z [auth A]	UA [auth C], Z [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain UA [auth C] Focus chain Z [auth A] Interactions & Density Focus chain UA [auth C] Focus chain Z [auth A]