8Y1V: GluN1b-GluN2D NMDA receptor

Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23. Determined by electron microscopy at 4.2 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 17,832
Mol. weight: 395.74 kDa
Ligands: NAG, A1LW8
Released: 22 Jan 2025

Explore 8Y1V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y1V contains 109 α-helices and 64 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	40-49	10
α-helix	72-80	9
α-helix	105-113	9
α-helix	118-119	2
β-strand	120	1	1
β-strand	139	1	1
α-helix	144-147	4
α-helix	149-157	9
β-strand	165	1	2
α-helix	171-183	13
β-strand	215	1	2
α-helix	226-233	8
β-strand	238-239	2	3
α-helix	246-257	12
β-strand	266-267	2	3
α-helix	272-277	6
α-helix	301-310	10
α-helix	338-348	11
β-strand	418	1	4
β-strand	426	1	5
β-strand	430	1	5
β-strand	431-433	3	6
β-strand	445	1	7
β-strand	451	1	7
β-strand	455-460	6	6
β-strand	471-477	7	6
α-helix	479-491	13
β-strand	494	1	4
α-helix	521-528	8
α-helix	542-547	6
β-strand	550	1	8
β-strand	559-563	5	9
α-helix	564-566	3
α-helix	581-599	19
α-helix	624-634	11
α-helix	654-676	23
α-helix	691-694	4
β-strand	702-703	2	9
α-helix	710-715	6
α-helix	718-720	3
α-helix	721-728	8
α-helix	735-743	9
β-strand	749-753	5	9
α-helix	754-763	10
β-strand	768-769	2	9
β-strand	782	1	8
α-helix	789-798	10
α-helix	800-814	15
α-helix	831-855	25

Chain B: 26 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	63-77	15
α-helix	99-106	8
α-helix	127-137	11
α-helix	168-182	15
α-helix	197-208	12
α-helix	230-237	8
α-helix	250-258	9
β-strand	307-309	3	10
α-helix	310-312	3
α-helix	316-335	20
α-helix	344-346	3
β-strand	366	1	11
β-strand	369	1	12
β-strand	372	1	12
β-strand	375	1	11
β-strand	376	1	13
β-strand	382	1	13
β-strand	387-389	3	10
β-strand	432-436	5	14
β-strand	444-446	3	15
α-helix	455-456	2
β-strand	483-485	3	15
α-helix	487-499	13
β-strand	503-507	5	14
α-helix	544-547	4
α-helix	583-585	3
α-helix	587-601	15
α-helix	630-639	10
α-helix	654-681	28
α-helix	719-723	5
α-helix	731-734	4
α-helix	743-747	5
α-helix	760-768	9
α-helix	800-806	7
α-helix	807-811	5
α-helix	812-822	11
α-helix	839-845	7
α-helix	849-863	15

Chain C: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	40-49	10
α-helix	72-80	9
α-helix	105-113	9
α-helix	118-119	2
β-strand	120	1	16
β-strand	139	1	16
α-helix	144-147	4
α-helix	149-157	9
α-helix	171-183	13
α-helix	226-234	9
β-strand	238-239	2	17
α-helix	246-261	16
β-strand	266-267	2	17
α-helix	272-276	5
α-helix	301-310	10
α-helix	338-348	11
β-strand	418	1	18
β-strand	426	1	19
β-strand	430	1	19
β-strand	431-433	3	20
β-strand	445	1	21
β-strand	451	1	21
β-strand	455-460	6	20
β-strand	471-477	7	20
α-helix	479-491	13
β-strand	494	1	18
α-helix	521-528	8
α-helix	542-547	6
β-strand	550	1	22
β-strand	559-563	5	23
α-helix	564-566	3
α-helix	581-599	19
α-helix	624-634	11
α-helix	654-676	23
α-helix	691-694	4
β-strand	702-703	2	23
α-helix	710-715	6
α-helix	718-720	3
α-helix	721-728	8
α-helix	735-743	9
β-strand	749-753	5	23
α-helix	754-763	10
β-strand	768-769	2	23
β-strand	782	1	22
α-helix	789-798	10
α-helix	800-814	15
α-helix	831-855	25

Chain D: 27 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	63-77	15
α-helix	99-106	8
α-helix	127-137	11
α-helix	168-182	15
α-helix	197-208	12
α-helix	230-237	8
α-helix	250-258	9
β-strand	307-309	3	24
α-helix	310-312	3
α-helix	316-335	20
α-helix	344-346	3
β-strand	366	1	25
β-strand	369	1	26
β-strand	372	1	26
β-strand	375	1	25
β-strand	376	1	27
β-strand	382	1	27
β-strand	387-389	3	24
β-strand	432-436	5	28
β-strand	444-446	3	29
α-helix	455-456	2
β-strand	483-485	3	29
α-helix	487-499	13
β-strand	503-507	5	28
α-helix	544-547	4
α-helix	583-585	3
α-helix	587-601	15
α-helix	630-639	10
α-helix	654-681	28
α-helix	719-723	5
α-helix	731-734	4
α-helix	743-747	5
α-helix	760-768	9
α-helix	800-806	7
α-helix	807-811	5
α-helix	812-822	11
α-helix	839-844	6
α-helix	845-847	3
α-helix	849-863	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 6 of Glutamate receptor ionotropic, NMDA 1	A, C	protein	868	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2D	B, D	protein	911	Homo sapiens	O15399 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8Y1V_1 Isoform 6 of Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL
ETLLEERESKSKKRNYENLDQLSYDNKRGPKAEKVLQFDPGTKNVTALLMEAKELEARVI
ILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESA
HISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVE
FNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLK
IVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFC
IDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTI
NNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYL
LDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGF
AMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVEL
STMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFG
IGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFML
VAGGIVAGIFLIFIEIAYKRHKDARRKQ

Sequence of entity 2 (B, D), FASTA

>8Y1V_2 Glutamate receptor ionotropic, NMDA 2D (chains B, D)
MRGAGGPRGPRGPAKMLLLLALACASPFPEEAPGPGGAGGPGGGLGGARPLNVALVFSGP
AYAAEAARLGPAVAAAVRSPGLDVRPVALVLNGSDPRSLVLQLCDLLSGLRVHGVVFEDD
SRAPAVAPILDFLSAQTSLPIVAVHGGAALVLTPKEKGSTFLQLGSSTEQQLQVIFEVLE
EYDWTSFVAVTTRAPGHRAFLSYIEVLTDGSLVGWEHRGALTLDPGAGEAVLSAQLRSVS
AQIRLLFCAREEAEPVFRAAEEAGLTGSGYVWFMVGPQLAGGGGSGAPGEPPLLPGGAPL
PAGLFAVRSAGWRDDLARRVAAGVAVVARGAQALLRDYGFLPELGHDCRAQNRTHRGESL
HRYFMNITWDNRDYSFNEDGFLVNPSLVVISLTRDRTWEVVGSWEQQTLRLKYPLWSRYG
RFLQPVDDTQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPE
KRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSL
TINEERSEIVDFSVPFVETGISVMVARSNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVT
VFIFEYLSPVGYNRSLATGKRPGGSTFTIGKSIWLLWALVFNNSVPVENPRGTTSKIMVL
VWAFFAVIFLASYTANLAAFMIQEEYVDTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEK
NIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGS
GKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICHNDKIEVMSSKL
DIDNMAGVFYMLLVAMGLSLLVFAWEHLVYWRLRHCLGPAASAWSHPQFEKGGGSGGGSG
GSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
A1LW8	(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R}…	C34 H56 O8	2

Primary citation

An antidepressant mechanism underlying the allosteric inhibition of GluN2D-incorporated NMDA receptors at GABAergic interneurons. Zhang, J., Duan, J., Li, W. et al. Sci Adv (2025) 11:eadq0444-eadq0444. DOI 10.1126/sciadv.adq0444 · PubMed

Other PDB entries of the same protein (UniProt Q05586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GJ1 1.62 Å, NMDA bound to compound 339
5H8F 1.81 Å, Structure of the apo human GluN1/GluN2A LBD
9GIC 1.82 Å, NMDA bound to compound 345
3BYA 1.85 Å, Structure of a Calmodulin Complex
5H8Q 1.9 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE8324
9GIF 1.9 Å, NMDA bound to compound 288
9GIB 1.95 Å, NMDA bound to compound 380
9MUM 1.97 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11,…
9GID 2.0 Å, NMDA bound to compound 338
5KCJ 2.09 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE6901
9GIG 2.09 Å, NMDA bound to compound 387
5I2N 2.12 Å, Structure of the human GluN1/GluN2A LBD in complex with…

Browse structure collections

About this viewer

MolViewer shows 8Y1V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.