8JIZ: GluN1-2A NMDAR

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab5F6 in two fab bind conformation. Determined by electron microscopy at 3.8 Å resolution. Released 5 Jun 2024.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 31,002
Mol. weight: 489.77 kDa
Ligands: NAG
Released: 5 Jun 2024

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

Secondary structure: helices and β-sheets

8JIZ contains 152 α-helices and 230 β-strands across 8 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: 27 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	37-40	4	1
α-helix	47-58	12
β-strand	70-73	4	1
α-helix	79-91	13
α-helix	92-94	3
β-strand	98-100	3	2
α-helix	108-120	13
β-strand	124-126	3	2
β-strand	144-146	3	2
α-helix	151-163	13
α-helix	164-166	3
β-strand	171-174	4	3
α-helix	178-180	3
α-helix	181-192	12
β-strand	205-207	3	3
β-strand	227-230	4	3
α-helix	233-245	13
β-strand	255-257	3	3
β-strand	276-279	4	3
α-helix	288-309	22
α-helix	335-338	4
β-strand	350	1	4
β-strand	355	1	2
β-strand	356	1	4
β-strand	362-366	5	3
β-strand	372-377	6	3
β-strand	408-410	3	5
β-strand	418-420	3	6
α-helix	421-423	3
β-strand	434-437	4	6
β-strand	453-457	5	6
α-helix	459-471	13
β-strand	477-479	3	5
β-strand	488-489	2	7
β-strand	492-493	2	7
α-helix	495-501	7
β-strand	507-508	2	5
α-helix	516-521	6
β-strand	523-524	2	5
β-strand	530-531	2	8
β-strand	533-535	3	9
β-strand	536-538	3	10
α-helix	561-578	18
α-helix	604-610	7
α-helix	627-631	5
α-helix	634-652	19
α-helix	668-671	4
β-strand	684	1	9
α-helix	690-697	8
α-helix	699-707	9
α-helix	714-721	8
β-strand	729-731	3	9
α-helix	732-740	9
β-strand	747-749	3	10
β-strand	759-760	2	8
β-strand	764-765	2	5
α-helix	772-784	13
α-helix	787-794	8
α-helix	815-836	22

Chain B: 34 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	27-32	6	11
α-helix	36-51	16
β-strand	60-62	3	11
β-strand	65	1	11
α-helix	71-82	12
β-strand	87-92	6	11
α-helix	105-111	7
β-strand	118-120	3	11
α-helix	127-129	3
β-strand	138-139	2	11
α-helix	145-158	14
β-strand	164-167	4	12
α-helix	171-186	16
β-strand	193-194	2	12
α-helix	205-212	8
β-strand	216	1	13
β-strand	218-222	5	12
α-helix	225-236	12
β-strand	246-247	2	12
α-helix	251-253	3
α-helix	256-260	5
α-helix	262-263	2
β-strand	267-271	5	14
α-helix	277-298	22
α-helix	302-305	4
α-helix	318-327	10
β-strand	330	1	15
β-strand	338	1	15
β-strand	340	1	16
β-strand	346	1	16
β-strand	351-357	7	14
β-strand	360-367	8	14
β-strand	372-374	3	14
β-strand	381	1	17
β-strand	385	1	17
α-helix	388-390	3
β-strand	392	1	13
β-strand	401	1	18
β-strand	410-412	3	19
α-helix	420-422	3
β-strand	424	1	20
α-helix	429	1
β-strand	430	1	20
α-helix	431-432	2
β-strand	434-436	3	19
β-strand	453-456	4	19
α-helix	458-470	13
β-strand	488	1	21
β-strand	497	1	21
α-helix	501-506	6
β-strand	513	1	18
β-strand	518	1	22
α-helix	521-526	6
β-strand	539-543	5	23
α-helix	544-547	4
α-helix	562-583	22
α-helix	605-614	10
α-helix	628-653	26
α-helix	670-673	4
β-strand	681-682	2	23
α-helix	688-695	8
α-helix	700-703	4
α-helix	705-707	3
α-helix	714-722	9
β-strand	728-731	4	23
α-helix	733-742	10
β-strand	746-749	4	23
β-strand	758	1	22
β-strand	761	1	18
α-helix	769-781	13
α-helix	784-792	9
α-helix	811-842	32

Chain C: 31 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	37-40	4	24
α-helix	46-55	10
α-helix	57-59	3
β-strand	71-73	3	24
α-helix	79-91	13
β-strand	98-100	3	24
α-helix	108-120	13
β-strand	124-126	3	24
α-helix	130-132	3
β-strand	144-146	3	24
α-helix	151-164	14
β-strand	169-170	2	25
β-strand	172-175	4	26
α-helix	180-192	13
α-helix	198	1
β-strand	199-200	2	25
β-strand	204-206	3	26
α-helix	214-221	8
β-strand	226-230	5	26
α-helix	233-245	13
β-strand	254-257	4	26
α-helix	273	1
β-strand	277-280	4	26
α-helix	288-309	22
β-strand	350	1	27
β-strand	356	1	27
β-strand	362-366	5	26
β-strand	372-374	3	26
β-strand	376-377	2	28
α-helix	380-382	3
β-strand	385-386	2	28
β-strand	407-410	4	29
β-strand	414	1	30
β-strand	417	1	30
β-strand	418	1	31
β-strand	434-438	5	29
β-strand	452-456	5	29
β-strand	457	1	31
α-helix	459-471	13
β-strand	476-479	4	29
β-strand	489	1	32
β-strand	492	1	32
α-helix	495-501	7
β-strand	507-508	2	29
α-helix	516-521	6
β-strand	524	1	29
β-strand	530-531	2	33
β-strand	533-538	6	34
α-helix	560-578	19
α-helix	604-610	7
α-helix	627-631	5
α-helix	634-651	18
α-helix	668-671	4
α-helix	673-675	3
α-helix	679-680	2
β-strand	684	1	35
α-helix	689-697	9
α-helix	699-707	9
β-strand	709	1	35
α-helix	713-722	10
β-strand	728-731	4	34
α-helix	732-740	9
α-helix	743-745	3
β-strand	747-749	3	34
β-strand	759-760	2	33
β-strand	764	1	29
α-helix	772-784	13
α-helix	787-792	6
α-helix	814-835	22

Chain D: 33 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	36
β-strand	29	1	37
β-strand	30-32	3	36
α-helix	35-51	17
β-strand	62	1	37
α-helix	71-82	12
α-helix	83-85	3
β-strand	87-92	6	36
α-helix	105-113	9
β-strand	118-120	3	36
α-helix	127-129	3
β-strand	138-139	2	36
α-helix	145-157	13
β-strand	163-168	6	38
α-helix	171-186	16
β-strand	194-197	4	38
α-helix	205-212	8
β-strand	218-222	5	38
α-helix	225-236	12
β-strand	247	1	38
α-helix	252-254	3
α-helix	257-260	4
α-helix	262-263	2
β-strand	269-271	3	39
α-helix	277-298	22
α-helix	302-305	4
α-helix	313-315	3
α-helix	318-327	10
β-strand	330-333	4	40
β-strand	336-338	3	40
β-strand	340	1	41
β-strand	346	1	41
β-strand	351-357	7	39
β-strand	360-367	8	39
β-strand	372-374	3	39
α-helix	378-380	3
β-strand	400-402	3	42
β-strand	412-413	2	42
β-strand	424	1	43
β-strand	430	1	43
β-strand	434-437	4	42
β-strand	452-455	4	42
α-helix	458-470	13
β-strand	477-478	2	42
β-strand	487	1	44
β-strand	498	1	44
α-helix	500-506	7
β-strand	512-516	5	42
α-helix	517-519	3
α-helix	521-524	4
β-strand	528-529	2	42
β-strand	538-543	6	45
α-helix	562-583	22
α-helix	605-614	10
α-helix	628-656	29
α-helix	661-664	4
α-helix	670-673	4
β-strand	676	1	46
β-strand	679	1	46
β-strand	681-682	2	45
α-helix	688-695	8
α-helix	700-705	6
α-helix	714-722	9
β-strand	728-732	5	45
α-helix	733-742	10
β-strand	746-753	8	45
β-strand	759-762	4	42
α-helix	770-781	12
α-helix	784-792	9
α-helix	811-842	32

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	47
β-strand	11	1	48
β-strand	17-25	9	47
α-helix	29-31	3
β-strand	34-39	6	49
β-strand	45-51	7	49
α-helix	62-64	3
β-strand	68-73	6	47
β-strand	78-84	7	47
α-helix	88-90	3
β-strand	92-98	7	49
β-strand	114	1	49
β-strand	118-120	3	49
β-strand	121	1	48
β-strand	128	1	50
β-strand	131-135	5	51
α-helix	136-138	3
α-helix	141-142	2
β-strand	146-156	11	51
β-strand	157	1	50
β-strand	162-165	4	52
α-helix	166-168	3
β-strand	170	1	52
β-strand	174-176	3	51
α-helix	177-179	3
β-strand	180-181	2	51
β-strand	187-196	10	51
α-helix	197-199	3
β-strand	205-211	7	52
β-strand	216-222	7	52

Chain F: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	53
β-strand	10-12	3	54
β-strand	19-24	6	53
β-strand	34-38	5	54
β-strand	45-49	5	54
β-strand	53-54	2	54
α-helix	55	1
β-strand	62-67	6	53
β-strand	70-75	6	53
α-helix	80-82	3
β-strand	85-90	6	54
α-helix	96	1
β-strand	97-98	2	54
β-strand	102-105	4	54
β-strand	114-118	5	55
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-137	9	55
β-strand	145-150	6	56
β-strand	153-155	3	56
β-strand	159-163	5	55
α-helix	164-167	4
β-strand	174-182	9	55
α-helix	183-187	5
β-strand	191-197	7	56
β-strand	205-210	6	56

Chain G: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	57
β-strand	11-12	2	58
β-strand	17-25	9	57
α-helix	29-31	3
β-strand	34-39	6	59
β-strand	45-51	7	59
β-strand	58-60	3	59
α-helix	62-64	3
β-strand	68-73	6	57
β-strand	78-84	7	57
α-helix	88-90	3
β-strand	92-98	7	59
β-strand	114	1	59
β-strand	118-120	3	59
β-strand	121-122	2	58
β-strand	128	1	60
β-strand	131-135	5	61
β-strand	146-156	11	61
β-strand	157	1	60
β-strand	161-165	5	62
α-helix	166-168	3
β-strand	170	1	62
β-strand	174-176	3	61
α-helix	177-179	3
β-strand	180-181	2	61
β-strand	187-196	10	61
β-strand	205-211	7	62
β-strand	216-222	7	62

Chain H: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	63
β-strand	10-12	3	59
β-strand	19-25	7	63
β-strand	33-38	6	59
β-strand	45-49	5	59
β-strand	53-54	2	59
α-helix	55	1
β-strand	62-65	4	63
β-strand	70-75	6	63
α-helix	80-82	3
β-strand	85-90	6	59
α-helix	96	1
β-strand	97-98	2	59
β-strand	102-105	4	59
β-strand	111	1	64
β-strand	114-118	5	65
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	65
β-strand	140	1	64
β-strand	145-150	6	66
β-strand	154-155	2	66
β-strand	159-163	5	65
α-helix	164-167	4
β-strand	173-182	10	65
α-helix	183-187	5
β-strand	191-197	7	66
β-strand	205-210	6	66

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 2A	A, C	protein	841	Homo sapiens	Q12879 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 1	B, D	protein	847	Homo sapiens	Q05586 (AlphaFold model)
Fab5F6 Heavy Chain	E, G	protein	259	Homo sapiens
Fab5F6 Light Chain	F, H	protein	236	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>8JIZ_1 Glutamate receptor ionotropic, NMDA 2A (chains A, C)
MGRVGYWTLLVLPALLVWRGPAPSAAAEKGPPALNIAVMLGHSHDVTERELRTLWGPEQA
AGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSHT
FVPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGY
REFISFVKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLIL
SEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGIGILT
TAASSMLEKFSYIPEAKASCYGQMERPEVPMHTLHPFMVNVTWDGKDLSFTEEGYQVHPR
LVVIVLNKDREWEKVGKWENHTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVE
DIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLV
TNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRS
NGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFT
IGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVD
QVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSL
KTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALL
QFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHL
F

Sequence of entity 2 (B, D), FASTA

>8JIZ_2 Glutamate receptor ionotropic, NMDA 1 (chains B, D)
MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNM
TGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA
DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDARRKQ

Sequence of entity 3 (E, G), FASTA

>8JIZ_3 Fab5F6 Heavy Chain (chains E, G)
MDWTWSILFLVAAPTGAHSEVQLVESGGGLVKPGGSLRLSCAASGFTLSDYYMSWIRQAP
GKGLEWISYISVSGTKIYYADSVKGRFTISRDNAKNSLFLEMNSLTAEDTAVYYCARDSG
STMYDGYNWFDPWGQGTLVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKR
VEPKSCDKTHTCPPCPAPE

Sequence of entity 4 (F, H), FASTA

>8JIZ_4 Fab5F6 Light Chain (chains F, H)
MDMRVPAQLLGLLLLWLRGARCDIQMTQSPSTLSASVGDRVTITCRASQSISRWLAWYQQ
KPGKAPKLLISLASDLQTGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQFDSYPLTF
GPGTTVDIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis. Wang, H., Xie, C., Deng, B. et al. Nat Struct Mol Biol (2024) 31:1987-1996. DOI 10.1038/s41594-024-01387-3 · PubMed

Other PDB entries of the same protein (UniProt Q12879 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5H8F 1.81 Å, Structure of the apo human GluN1/GluN2A LBD
5H8Q 1.9 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE8324
3NFL 1.91 Å, Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A…
9MUM 1.97 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11,…
5KCJ 2.09 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE6901
5I2N 2.12 Å, Structure of the human GluN1/GluN2A LBD in complex with…
5H8H 2.23 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE3419
5TP9 2.4 Å, Structure of the human GluN1/GluN2A LBD in complex with compound 2 (GNE9178)
9MUL 2.4 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 1,…
5KDT 2.44 Å, Structure of the human GluN1/GluN2A LBD in complex with GNE0723
5TPA 2.48 Å, Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500)
5H8N 2.5 Å, Structure of the human GluN1/GluN2A LBD in complex with NAM

Browse structure collections

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