8Y1V | pdb_00008y1v

Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23

PDB DOI: https://doi.org/10.2210/pdb8Y1V/pdb
EM Map EMD-38847: EMDB EMDataResource

Classification: MEMBRANE PROTEIN/INHIBITOR
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-01-25 Released: 2025-01-22
Deposition Author(s): Zhang, J.L., Zhu, S.J., Guo, F.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A novel antidepressant acting via allosteric inhibition of GluN2D-incorporated NMDA receptors at GABAergic interneurons

Zhang, J.L., Zhu, S.J., Fei, G.

To be published.

Macromolecule Content

Total Structure Weight: 395.74 kDa
Atom Count: 17,832
Modeled Residue Count: 2,760
Deposited Residue Count: 3,558
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 6 of Glutamate receptor ionotropic, NMDA 1	A, C	868	Homo sapiens	Mutation(s): 0 Gene Names: GRIN1, NMDAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens) Explore Q05586 Go to UniProtKB: Q05586
PHAROS: Q05586 GTEx: ENSG00000176884
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05586
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C	Go to GlyGen: Q05586-1
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 2D	B, D	911	Homo sapiens	Mutation(s): 0 Gene Names: GRIN2D, GluN2D, NMDAR2D
UniProt & NIH Common Fund Data Resources
Find proteins for O15399 (Homo sapiens) Explore O15399 Go to UniProtKB: O15399
PHAROS: O15399 GTEx: ENSG00000105464
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15399
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LW8 (Subject of Investigation/LOI) Query on A1LW8 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D] mmCIF format, chain G [auth B] mmCIF format, chain J [auth D]	G [auth B], J [auth D]	(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol C₃₄ H₅₆ O₈ ULNDCEKFZLEEGC-TWIDTKOTSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C]	E [auth A], F [auth A], H [auth C], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C]

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
RECONSTRUCTION	RELION	3.1.1
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Zhang, J.L.

Zhu, S.J.

Guo, F.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31771115
National Natural Science Foundation of China (NSFC)	China	31671049
National Natural Science Foundation of China (NSFC)	China	81030065
Chinese Academy of Sciences	China	XDB32020000
Chinese Academy of Sciences	China	XDA12040214
Chinese Academy of Sciences	China	XDA12040220
National Natural Science Foundation of China (NSFC)	China	81803828
Chinese Academy of Sciences	China	2019280
National Natural Science Foundation of China (NSFC)	China	32221003