7YFO: Glutamate receptor ionotropic, NMDA 1

Structure of GluN1a E698C-GluN2D NMDA receptor in cystines crosslinked state. Determined by electron microscopy at 6.4 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 6.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 18,274
Mol. weight: 384.87 kDa
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

7YFO contains 116 α-helices and 150 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: 27 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	1
α-helix	38-52	15
β-strand	61-65	5	1
α-helix	71-84	14
β-strand	91-92	2	1
α-helix	104-113	10
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-158	15
β-strand	163-168	6	2
α-helix	171-187	17
β-strand	194-197	4	2
α-helix	205-212	8
β-strand	216	1	3
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-249	4	2
α-helix	258-261	4
α-helix	263	1
β-strand	267-271	5	2
α-helix	277-296	20
α-helix	314-315	2
α-helix	317-327	11
β-strand	330-333	4	4
β-strand	336-338	3	4
β-strand	340	1	5
β-strand	346	1	5
β-strand	351-357	7	2
β-strand	360-368	9	2
β-strand	371-373	3	2
β-strand	392	1	3
α-helix	393-394	2
β-strand	398-402	5	6
β-strand	410-413	4	7
β-strand	424	1	8
α-helix	429	1
β-strand	430	1	8
α-helix	431	1
β-strand	434-436	3	7
β-strand	437	1	6
β-strand	440	1	9
β-strand	450	1	9
β-strand	453-456	4	7
α-helix	458-470	13
β-strand	474-478	5	6
β-strand	488	1	10
β-strand	497	1	10
α-helix	500-507	8
β-strand	512-518	7	6
α-helix	519	1
α-helix	521-524	4
β-strand	527-529	3	6
β-strand	534-536	3	6
β-strand	538-542	5	11
α-helix	670-673	4
β-strand	681-682	2	11
β-strand	684	1	12
α-helix	688-695	8
α-helix	700-709	10
β-strand	711	1	12
α-helix	714-722	9
β-strand	728-732	5	11
α-helix	733-743	11
β-strand	747-749	3	11
β-strand	756-763	8	6
α-helix	767-782	16
α-helix	784-792	9

Chains B and D: 31 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	13
α-helix	60-62	3
α-helix	63-68	6
α-helix	71-73	3
α-helix	79-81	3
β-strand	87-90	4	13
α-helix	96-110	15
β-strand	114-118	5	13
α-helix	124-126	3
α-helix	127-137	11
β-strand	141-144	4	13
α-helix	147-150	4
α-helix	168-182	15
β-strand	185-191	7	14
α-helix	197-211	15
β-strand	214-220	7	14
α-helix	231-237	7
β-strand	243-247	5	14
α-helix	250-262	13
β-strand	271-273	3	14
α-helix	276-280	5
α-helix	299-300	2
β-strand	304-309	6	14
α-helix	310-312	3
α-helix	316-338	23
α-helix	352-355	4
α-helix	360-363	4
β-strand	368-369	2	15
β-strand	372-373	2	15
β-strand	376	1	16
β-strand	382	1	16
β-strand	386-392	7	14
β-strand	398	1	14
β-strand	402-405	4	14
β-strand	408-411	4	14
β-strand	431-432	2	17
β-strand	434-436	3	18
β-strand	444-446	3	19
β-strand	460-462	3	19
β-strand	463	1	18
β-strand	482-485	4	19
α-helix	487-499	13
β-strand	502-503	2	17
β-strand	506-507	2	18
β-strand	516-517	2	20
β-strand	520-521	2	20
α-helix	523-528	6
β-strand	535-536	2	18
β-strand	541	1	21
α-helix	544-547	4
β-strand	552	1	22
β-strand	557-565	9	21
α-helix	692-694	3
α-helix	696-699	4
α-helix	712-713	2
α-helix	717-725	9
α-helix	727-732	6
α-helix	741-749	9
β-strand	755-759	5	21
α-helix	760-769	10
α-helix	774-776	3
β-strand	784-789	6	21
β-strand	792	1	22
α-helix	800-813	14
α-helix	817-824	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	847	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

>7YFO_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNM
TGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA
DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVCLSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDARRKQ

Sequence of entity 2 (B, D), FASTA

>7YFO_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…

Browse structure collections

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