7YFM: GluN1b-GluN2D NMDA receptor

Structure of GluN1b-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Determined by electron microscopy at 5.1 Å resolution. Released 29 Mar 2023.

Method: Electron microscopy
Resolution: 5.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 18,836
Mol. weight: 390.01 kDa
Released: 29 Mar 2023

Explore 7YFM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YFM contains 104 α-helices and 124 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.

Chains A and C: 25 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	37-51	15
α-helix	71-84	14
β-strand	92	1	1
α-helix	104-113	10
β-strand	118-119	2	2
β-strand	120	1	1
α-helix	126-129	4
β-strand	137-138	2	2
α-helix	144-157	14
β-strand	164-167	4	3
α-helix	171-185	15
α-helix	226-233	8
β-strand	237	1	4
β-strand	239-243	5	3
α-helix	246-258	13
β-strand	267-269	3	3
α-helix	272-279	8
β-strand	287	1	5
β-strand	291-292	2	6
α-helix	298-316	19
α-helix	338-347	10
α-helix	351-353	3
β-strand	361	1	7
β-strand	367	1	7
β-strand	372-374	3	6
β-strand	377-378	2	5
β-strand	381-382	2	5
β-strand	386-389	4	6
β-strand	392-395	4	6
β-strand	413	1	4
β-strand	422-423	2	8
β-strand	430-434	5	9
β-strand	455-457	3	9
α-helix	460	1
β-strand	461	1	10
α-helix	462	1
β-strand	471	1	10
β-strand	474-478	5	9
α-helix	479-491	13
β-strand	498-499	2	8
β-strand	508-510	3	11
β-strand	517-519	3	11
α-helix	521-528	8
β-strand	533-534	2	12
α-helix	542-547	6
β-strand	550	1	12
β-strand	555-557	3	13
β-strand	559-563	5	14
α-helix	660-676	17
α-helix	691-694	4
β-strand	702-703	2	14
β-strand	704-705	2	15
α-helix	710-717	8
α-helix	721-729	9
β-strand	731-732	2	15
α-helix	735-743	9
β-strand	749-753	5	14
α-helix	754-764	11
β-strand	768-769	2	14
β-strand	777-779	3	13
β-strand	782-783	2	12
α-helix	788-803	16
α-helix	805-814	10

Chains B and D: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	64-69	6
α-helix	71-77	7
α-helix	96-108	13
β-strand	117	1	16
α-helix	126-137	12
β-strand	143	1	16
α-helix	168-181	14
β-strand	188-191	4	17
α-helix	195-208	14
α-helix	228-235	8
β-strand	243-247	5	17
α-helix	253-257	5
α-helix	260-262	3
β-strand	271-273	3	17
β-strand	304-309	6	17
α-helix	316-334	19
α-helix	336-338	3
α-helix	360-363	4
α-helix	369-371	3
β-strand	376	1	18
α-helix	381	1
β-strand	382	1	18
β-strand	387-392	6	17
β-strand	398-405	8	17
β-strand	408-411	4	17
α-helix	418-420	3
β-strand	431-436	6	19
β-strand	444-447	4	20
α-helix	448-449	2
β-strand	460	1	20
β-strand	482-485	4	20
α-helix	487-499	13
β-strand	502-507	6	19
β-strand	517	1	21
β-strand	520	1	21
α-helix	523-529	7
β-strand	535-536	2	19
β-strand	541	1	22
α-helix	544-550	7
β-strand	557-564	8	22
α-helix	662-680	19
α-helix	696-699	4
α-helix	717-725	9
α-helix	727-732	6
α-helix	741-749	9
β-strand	756-759	4	22
α-helix	760-769	10
β-strand	784-789	6	22
β-strand	792	1	19
α-helix	800-812	13
α-helix	816-823	8

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	891	Homo sapiens	O15399 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7YFM_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

>7YFM_2 Glutamate receptor ionotropic, NMDA 2D (chains B, D)
MRGAGGPRGPRGPAKMLLLLALACASPFPEEAPGPGGAGGPGGGLGGARPLNVALVFSGP
AYAAEAARLGPAVAAAVRSPGLDVRPVALVLNGSDPRSLVLQLCDLLSGLRVHGVVFEDD
SRAPAVAPILDFLSAQTSLPIVAVHGGAALVLTPKEKGSTFLQLGSSTEQQLQVIFEVLE
EYDWTSFVAVTTRAPGHRAFLSYIEVLTDGSLVGWEHRGALTLDPGAGEAVLSAQLRSVS
AQIRLLFCAREEAEPVFRAAEEAGLTGSGYVWFMVGPQLAGGGGSGAPGEPPLLPGGAPL
PAGLFAVRSAGWRDDLARRVAAGVAVVARGAQALLRDYGFLPELGHDCRAQNRTHRGESL
HRYFMNITWDNRDYSFNEDGFLVNPSLVVISLTRDRTWEVVGSWEQQTLRLKYPLWSRYG
RFLQPVDDTQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPE
KRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSL
TINEERSEIVDFSVPFVETGISVMVARSNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVT
VFIFEYLSPVGYNRSLATGKRPGGSTFTIGKSIWLLWALVFNNSVPVENPRGTTSKIMVL
VWAFFAVIFLASYTANLAAFMIQEEYVDTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEK
NIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGS
GKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICHNDKIEVMSSKL
DIDNMAGVFYMLLVAMGLSLLVFAWEHLVYWRLRHCLGPAASAWSHPQFEK

Primary citation

Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits. Zhang, J., Zhang, M., Wang, Q. et al. Nat Struct Mol Biol (2023) 30:629-639. DOI 10.1038/s41594-023-00959-z · 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…

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