8E96: Glutamate receptor ionotropic, NMDA 1

Glycine and glutamate bound Human GluN1a-GluN2D NMDA receptor. Determined by electron microscopy at 3.38 Å resolution. Released 7 Dec 2022.

Method: Electron microscopy
Resolution: 3.38 Å
Organism: Homo sapiens
Chains: 4
Atoms: 21,924
Mol. weight: 381.45 kDa
Ligands: GLY, NAG, GLU
Released: 7 Dec 2022

Explore 8E96 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E96 contains 121 α-helices and 172 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: 33 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	1
α-helix	36-52	17
β-strand	59-62	4	1
α-helix	66-68	3
α-helix	74-77	4
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	104-110	7
α-helix	112-114	3
β-strand	118-120	3	1
β-strand	138-139	2	1
α-helix	147-157	11
β-strand	164-167	4	2
α-helix	171-184	14
α-helix	185-187	3
β-strand	193-196	4	2
α-helix	206-211	6
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-248	3	2
α-helix	257-261	5
α-helix	262-263	2
β-strand	267	1	2
β-strand	270-271	2	3
α-helix	277-295	19
α-helix	302-305	4
α-helix	319-325	7
β-strand	330	1	4
β-strand	338	1	4
β-strand	341	1	5
β-strand	345	1	5
β-strand	351-357	7	3
β-strand	360-367	8	3
β-strand	372-373	2	3
α-helix	380	1
β-strand	381	1	6
β-strand	385	1	6
α-helix	388-389	2
β-strand	397-402	6	7
β-strand	405	1	8
β-strand	409	1	8
β-strand	410-413	4	7
β-strand	425	1	9
β-strand	428	1	9
β-strand	434-437	4	7
β-strand	439	1	10
β-strand	450	1	10
β-strand	453-456	4	7
α-helix	460-470	11
β-strand	473-478	6	7
β-strand	488-489	2	11
β-strand	496-497	2	11
α-helix	502-505	4
β-strand	512-513	2	7
α-helix	521-524	4
β-strand	527-528	2	12
β-strand	538-543	6	13
α-helix	561-581	21
α-helix	604-614	11
α-helix	627-654	28
α-helix	670-673	4
β-strand	681-682	2	13
β-strand	684	1	14
α-helix	688-694	7
α-helix	700-703	4
β-strand	711	1	14
α-helix	714-722	9
β-strand	728-732	5	13
α-helix	736-742	7
β-strand	746-748	3	13
β-strand	761	1	7
β-strand	762-763	2	12
α-helix	769-781	13
α-helix	785-788	4
α-helix	789-794	6

Chain B: 27 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	49	1	15
β-strand	54-58	5	16
α-helix	60-64	5
α-helix	69-76	8
β-strand	82	1	15
β-strand	87-91	5	16
α-helix	99-107	9
β-strand	115-117	3	16
α-helix	127-137	11
β-strand	141-143	3	16
β-strand	162-163	2	16
α-helix	168-171	4
α-helix	174-181	8
β-strand	186-191	6	17
α-helix	197-208	12
β-strand	216-222	7	17
α-helix	229-236	8
β-strand	243-247	5	17
α-helix	253-263	11
β-strand	271-274	4	17
β-strand	304-305	2	17
β-strand	306-309	4	18
α-helix	310-313	4
α-helix	316-329	14
α-helix	332-337	6
α-helix	359-363	5
β-strand	367-369	3	19
β-strand	372-374	3	19
β-strand	387-390	4	18
β-strand	400-405	6	18
β-strand	408-411	4	18
β-strand	419	1	20
β-strand	422	1	20
β-strand	431-436	6	21
β-strand	439	1	22
β-strand	443	1	22
β-strand	444-446	3	23
β-strand	460-461	2	23
β-strand	483-485	3	23
α-helix	487-498	12
β-strand	502-507	6	21
β-strand	515-517	3	24
β-strand	520-522	3	24
α-helix	524-529	6
β-strand	535-536	2	21
α-helix	544-547	4
β-strand	551-552	2	21
β-strand	558-561	4	25
β-strand	562-566	5	26
α-helix	634-640	7
α-helix	656-680	25
α-helix	696-699	4
α-helix	701-704	4
α-helix	718-723	6
α-helix	727-733	7
α-helix	743-750	8
β-strand	756-758	3	26
α-helix	763-766	4
β-strand	775-777	3	26
β-strand	784-788	5	25
β-strand	792-793	2	21
α-helix	800-812	13
α-helix	820-823	4
α-helix	849-861	13

Chain C: 32 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	27
α-helix	36-53	18
β-strand	61	1	27
β-strand	64-66	3	27
α-helix	72-81	10
α-helix	83-85	3
β-strand	87-93	7	27
α-helix	104-110	7
α-helix	112-114	3
β-strand	118-121	4	27
β-strand	137-139	3	27
α-helix	144-147	4
α-helix	148-157	10
β-strand	164	1	28
β-strand	165-166	2	29
β-strand	167-168	2	30
α-helix	171-184	14
β-strand	193	1	28
β-strand	196-197	2	30
α-helix	206-211	6
β-strand	220-221	2	29
α-helix	227-237	11
β-strand	249	1	29
α-helix	252-254	3
α-helix	256-259	4
β-strand	267-268	2	29
α-helix	278-293	16
α-helix	319-321	3
α-helix	322-326	5
β-strand	330	1	31
β-strand	338	1	31
β-strand	340	1	32
β-strand	346	1	32
β-strand	354-357	4	29
β-strand	360-363	4	29
β-strand	365	1	33
β-strand	375	1	33
α-helix	388-390	3
β-strand	397-402	6	34
β-strand	411-413	3	35
α-helix	420-422	3
α-helix	431-432	2
β-strand	434	1	35
β-strand	437-438	2	36
β-strand	451-452	2	36
β-strand	453-455	3	35
α-helix	460-469	10
β-strand	473-478	6	34
β-strand	487-488	2	37
β-strand	497-498	2	37
α-helix	502-505	4
β-strand	512-513	2	34
β-strand	518	1	38
α-helix	521-524	4
β-strand	527-528	2	39
β-strand	535-536	2	40
β-strand	538-543	6	41
α-helix	561-574	14
α-helix	604-606	3
α-helix	609-614	6
α-helix	628-654	27
α-helix	670-673	4
β-strand	681-682	2	41
β-strand	684	1	42
α-helix	688-692	5
α-helix	697-699	3
β-strand	711	1	42
α-helix	714-722	9
β-strand	728-732	5	41
α-helix	733-743	11
β-strand	746-749	4	41
β-strand	756-757	2	40
β-strand	758	1	38
β-strand	761	1	34
β-strand	762-763	2	39
α-helix	769-782	14
α-helix	784-792	9

Chain D: 29 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	43
β-strand	54-55	2	44
α-helix	60-63	4
α-helix	69-72	4
β-strand	79	1	45
β-strand	82	1	45
β-strand	83-84	2	43
β-strand	87-88	2	44
α-helix	98-109	12
β-strand	115-117	3	44
α-helix	124-126	3
α-helix	127-135	9
β-strand	141-143	3	44
α-helix	147-149	3
α-helix	155-156	2
β-strand	161-162	2	44
α-helix	173-176	4
β-strand	186-191	6	46
α-helix	197-208	12
β-strand	216-222	7	46
α-helix	229-236	8
β-strand	243-247	5	46
α-helix	253-262	10
β-strand	271-274	4	46
β-strand	304-308	5	46
α-helix	316-337	22
α-helix	358-363	6
β-strand	368-369	2	47
β-strand	372-373	2	47
β-strand	376	1	48
β-strand	382	1	48
β-strand	388-393	6	46
β-strand	397-400	4	46
β-strand	402-405	4	49
β-strand	408-411	4	49
β-strand	416	1	50
β-strand	419	1	50
β-strand	434-435	2	51
β-strand	439	1	52
β-strand	443	1	52
β-strand	444-447	4	53
α-helix	448-449	2
β-strand	460-461	2	53
β-strand	462	1	51
β-strand	482-485	4	53
α-helix	487-499	13
β-strand	505	1	51
β-strand	516-517	2	54
β-strand	520-521	2	54
α-helix	523-529	7
β-strand	535-536	2	51
β-strand	541	1	55
α-helix	544-547	4
β-strand	551	1	56
β-strand	558-561	4	57
β-strand	562-566	5	58
α-helix	653-676	24
α-helix	677-679	3
α-helix	696-699	4
α-helix	718-725	8
α-helix	727-733	7
α-helix	734-736	3
α-helix	741-749	9
β-strand	756-758	3	58
α-helix	760-768	9
β-strand	769	1	59
α-helix	771-773	3
β-strand	775-777	3	58
β-strand	784-788	5	57
β-strand	789	1	55
β-strand	792	1	51
β-strand	793	1	56
α-helix	800-812	13
α-helix	815-823	9
β-strand	827	1	59
α-helix	847-861	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	829	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2D	B, D	protein	887	Homo sapiens	O15399 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8E96_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
RAASDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSV
CEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFL
RTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFD
PGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNA
LRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTG
PLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRK
IIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTG
PNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEW
NGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPF
QSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSG
IGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDK
FIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEF
EASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQEC
DSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDANGAQ

Sequence of entity 2 (B, D), FASTA

>8E96_2 Glutamate receptor ionotropic, NMDA 2D (chains B, D)
WSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRGFPEEAPGPGGAGGPGGGLGGARPLN
VALVFSGPAYAAEAARLGPAVAAAVRSPGLDVRPVALVLNGSDPRSLVLQLCDLLSGLRV
HGVVFEDDSRAPAVAPILDFLSAQTSLPIVAVHGGAALVLTPKEKGSTFLQLGSSTEQQL
QVIFEVLEEYDWTSFVAVTTRAPGHRAFLSYIEVLTDGSLVGWEHRGALTLDPGAGEAVL
SAQLRSVSAQIRLLFCAREEAEPVFRAAEEAGLTGSGYVWFMVGPQLAGGGGSGAPGEPP
LLPGGAPLPAGLFAVRSAGWRDDLARRVAAGVAVVARGAQALLRDYGFLPELGHDCRAQN
RTHRGESLHRYFMNITWDNRDYSFNEDGFLVNPSLVVISLTRDRTWEVVGSWEQQTLRLK
YPLWSRYGRFLQPVDDTQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQLNRTHSP
PPDAPRPEKRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQR
ADMAIGSLTINEERSEIVDFSVPFVETGISVMVARSNGTVSPSAFLEPYSPAVWVMMFVM
CLTVVAVTVFIFEYLSPVGYNRSLATGKRPGGSTFTIGKSIWLLWALVFNNSVPVENPRG
TTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYVDTVSGLSDRKFQRPQEQYPPLKFGT
VPNGSTEKNIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEG
CKLVTIGSGKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICHNDK
IEVMSSKLDIDNMAGVFYMLLVAMGLSLLVFAWEHLVYWRLRHCLGP

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
GLU	Glutamic acid	C5 H9 N O4	2

Primary citation

Structural insights into assembly and function of GluN1-2C, GluN1-2A-2C, and GluN1-2D NMDARs. Chou, T.H., Kang, H., Simorowski, N. et al. Mol Cell (2022) 82:4548. DOI 10.1016/j.molcel.2022.10.008 · 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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