8VUT: Human GluN1-2A with IgG 008-218

Human GluN1-2A with IgG 008-218. Determined by electron microscopy at 3.7 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 28,819
Mol. weight: 456.75 kDa
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8VUT contains 125 α-helices and 234 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, 44 β-strands

Element	Residues	Length	Sheet
β-strand	28-29	2	1
β-strand	30-31	2	2
β-strand	32-33	2	3
α-helix	36-51	16
β-strand	61-62	2	1
β-strand	65-66	2	3
α-helix	72-83	12
β-strand	90-91	2	2
α-helix	105-113	9
β-strand	118-120	3	2
β-strand	138-139	2	2
α-helix	146-158	13
β-strand	163-167	5	4
α-helix	172-184	13
β-strand	195	1	4
α-helix	205-212	8
β-strand	218-222	5	4
α-helix	225-237	13
β-strand	246-249	4	4
β-strand	267	1	4
β-strand	271	1	5
α-helix	277-296	20
α-helix	303-305	3
α-helix	318-326	9
β-strand	333	1	6
β-strand	336	1	6
β-strand	340-341	2	7
β-strand	344-346	3	7
β-strand	351	1	5
β-strand	354	1	8
β-strand	363	1	8
β-strand	365-367	3	5
β-strand	372-374	3	5
β-strand	400	1	9
β-strand	401	1	10
β-strand	405	1	11
β-strand	409	1	11
β-strand	412	1	12
α-helix	413-415	3
α-helix	429-432	4
β-strand	434-436	3	12
β-strand	453-455	3	12
α-helix	458-470	13
β-strand	477	1	10
β-strand	488-489	2	13
β-strand	496-497	2	13
α-helix	500-506	7
β-strand	512	1	9
α-helix	522-525	4
β-strand	528	1	14
β-strand	538	1	15
β-strand	539-541	3	16
β-strand	542-543	2	17
α-helix	560-580	21
α-helix	584-595	12
α-helix	608-637	30
α-helix	651-654	4
β-strand	662	1	18
α-helix	669-676	8
α-helix	681-687	7
α-helix	695-703	9
β-strand	709	1	18
β-strand	710-712	3	16
α-helix	714-723	10
β-strand	727-728	2	17
β-strand	734	1	15
β-strand	743	1	14
α-helix	750-764	15
α-helix	766-773	8
α-helix	783-796	14
α-helix	799-811	13

Chain B: 24 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	37-40	4	19
β-strand	70-73	4	19
α-helix	79-91	13
β-strand	98-100	3	19
α-helix	109-118	10
β-strand	125	1	20
β-strand	126	1	19
α-helix	130-132	3
β-strand	145	1	20
α-helix	151-164	14
β-strand	171-174	4	21
α-helix	180-191	12
β-strand	203-205	3	21
α-helix	213-219	7
β-strand	227-230	4	21
α-helix	233-244	12
β-strand	255-257	3	21
α-helix	259-262	4
β-strand	277-281	5	21
α-helix	288-309	22
β-strand	342	1	22
β-strand	347	1	22
β-strand	361-365	5	21
β-strand	366	1	23
β-strand	372	1	23
α-helix	400-402	3
β-strand	405-410	6	24
β-strand	413	1	25
β-strand	417	1	25
β-strand	418-420	3	24
β-strand	434-438	5	24
β-strand	452-457	6	24
α-helix	459-471	13
β-strand	474-479	6	24
β-strand	489	1	26
β-strand	492	1	26
α-helix	495-501	7
β-strand	513	1	27
α-helix	517-521	5
β-strand	534-537	4	28
α-helix	556-577	22
α-helix	581-593	13
α-helix	606-634	29
α-helix	653-655	3
β-strand	663	1	28
β-strand	664	1	29
α-helix	670-677	8
α-helix	679-685	7
β-strand	689	1	29
α-helix	694-701	8
β-strand	707-710	4	28
α-helix	713-720	8
β-strand	728-729	2	28
β-strand	741	1	27
α-helix	752-764	13
α-helix	767-775	9
α-helix	791-813	23

Chain C: 31 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	28-29	2	30
β-strand	32-33	2	31
α-helix	36-52	17
β-strand	61-62	2	30
β-strand	65-66	2	31
α-helix	72-83	12
β-strand	87	1	30
β-strand	90-92	3	31
α-helix	100-102	3
α-helix	105-113	9
β-strand	118-120	3	31
β-strand	138	1	31
α-helix	145-157	13
β-strand	166-167	2	32
α-helix	172-185	14
β-strand	195-196	2	32
α-helix	205-212	8
β-strand	220-221	2	33
α-helix	225-237	13
β-strand	248-249	2	33
α-helix	251-254	4
α-helix	258-261	4
β-strand	267-271	5	33
α-helix	277-295	19
α-helix	303-305	3
α-helix	318-327	10
β-strand	332	1	34
β-strand	337	1	34
β-strand	340-341	2	35
β-strand	344-346	3	35
β-strand	351-355	5	33
β-strand	363-367	5	33
β-strand	372-374	3	33
β-strand	398	1	36
β-strand	410-412	3	37
α-helix	413-415	3
β-strand	424	1	38
β-strand	430	1	38
α-helix	431-432	2
β-strand	434-436	3	37
β-strand	453-456	4	37
α-helix	458-469	12
β-strand	474	1	36
β-strand	487-489	3	39
α-helix	490	1
β-strand	496-498	3	39
α-helix	500-506	7
α-helix	521-524	4
β-strand	541-543	3	40
α-helix	544-546	3
α-helix	560-579	20
α-helix	584-594	11
α-helix	608-637	30
α-helix	651-654	4
α-helix	670-676	7
α-helix	678-688	11
α-helix	696-703	8
α-helix	714-723	10
β-strand	727-729	3	40
α-helix	750-763	14
α-helix	765-773	9
α-helix	789-812	24

Chain D: 25 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	37-40	4	41
β-strand	70-73	4	41
α-helix	79-91	13
β-strand	98-99	2	41
α-helix	109-118	10
β-strand	125-126	2	41
β-strand	145-146	2	41
α-helix	151-164	14
β-strand	170	1	42
β-strand	171	1	43
β-strand	172-173	2	42
β-strand	174	1	44
α-helix	180-191	12
β-strand	200-204	5	42
α-helix	213-219	7
β-strand	226-227	2	43
β-strand	230	1	44
α-helix	233-246	14
β-strand	254-255	2	43
β-strand	256-257	2	45
α-helix	259-261	3
β-strand	277-280	4	45
α-helix	288-309	22
α-helix	336-338	3
β-strand	341-342	2	46
β-strand	347-348	2	46
β-strand	362-364	3	45
β-strand	405-406	2	47
β-strand	408	1	48
β-strand	409-410	2	49
β-strand	413	1	50
β-strand	417	1	50
β-strand	418-420	3	51
α-helix	421-423	3
β-strand	434-436	3	51
β-strand	439	1	52
α-helix	444-447	4
β-strand	451	1	52
β-strand	454-457	4	51
α-helix	459-471	13
β-strand	474-475	2	47
β-strand	478-479	2	49
β-strand	487-488	2	53
β-strand	493-494	2	53
α-helix	497-501	5
β-strand	507	1	48
β-strand	513	1	54
α-helix	518-520	3
β-strand	534-538	5	55
α-helix	557-577	21
α-helix	580-593	14
α-helix	605-632	28
α-helix	648-651	4
β-strand	663	1	55
α-helix	670-677	8
α-helix	686-688	3
α-helix	694-701	8
β-strand	708-710	3	55
α-helix	712-720	9
β-strand	727-729	3	55
β-strand	741	1	54
α-helix	752-764	13
α-helix	767-775	9
α-helix	787-813	27

Chain H: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	56
β-strand	11-12	2	57
β-strand	17-25	9	56
β-strand	34-39	6	58
β-strand	45-50	6	58
β-strand	59-60	2	58
β-strand	68-73	6	56
β-strand	78-84	7	56
β-strand	93-94	2	59
β-strand	95-99	5	58
α-helix	104-106	3
β-strand	109-110	2	58
β-strand	116-117	2	59
β-strand	119-120	2	57
β-strand	129-133	5	60
β-strand	144-154	11	60
β-strand	160-163	4	61
α-helix	164-166	3
β-strand	172-174	3	60
α-helix	175-177	3
β-strand	178-179	2	60
β-strand	185-194	10	60
α-helix	195-197	3
β-strand	204-209	6	61
β-strand	214-219	6	61

Chain I: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	62
β-strand	11-12	2	63
β-strand	17-25	9	62
β-strand	34-39	6	64
β-strand	45-50	6	64
β-strand	59-60	2	64
β-strand	68-73	6	62
β-strand	78-84	7	62
α-helix	88-90	3
β-strand	92	1	65
β-strand	95-98	4	64
β-strand	110	1	64
β-strand	118	1	65
β-strand	119-120	2	63
β-strand	126	1	66
β-strand	129-133	5	67
β-strand	144-154	11	67
β-strand	155	1	66
β-strand	160-163	4	68
α-helix	164-166	3
β-strand	172-174	3	67
β-strand	178-179	2	67
β-strand	185-194	10	67
α-helix	195-197	3
β-strand	204-209	6	68
β-strand	214-219	6	68

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	69
β-strand	9-12	4	70
β-strand	18-23	6	69
α-helix	29-31	3
β-strand	35-38	4	70
β-strand	46-49	4	70
β-strand	50	1	71
β-strand	54	1	71
β-strand	64-66	3	69
β-strand	73-78	6	69
β-strand	88-92	5	70
β-strand	97	1	70
β-strand	101-105	5	70
α-helix	109-110	2
β-strand	111	1	72
β-strand	114-118	5	73
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	73
β-strand	140	1	72
β-strand	144-149	6	74
β-strand	154-155	2	74
β-strand	159-161	3	73
α-helix	162-164	3
β-strand	165-166	2	73
β-strand	172-180	9	73
α-helix	182-187	6
β-strand	191-197	7	74
β-strand	200-206	7	74

Chain M: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	75
β-strand	9-12	4	76
β-strand	18-24	7	75
β-strand	35-39	5	76
β-strand	46-49	4	76
β-strand	65-66	2	75
β-strand	73-78	6	75
β-strand	88-92	5	76
β-strand	101-105	5	76
α-helix	109-110	2
β-strand	111	1	77
β-strand	114-118	5	78
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	78
β-strand	140	1	77
β-strand	144-149	6	79
β-strand	154-155	2	79
β-strand	160-161	2	78
α-helix	162-164	3
β-strand	165-166	2	78
β-strand	172-180	9	78
α-helix	182-187	6
β-strand	191-197	7	79
β-strand	200-206	7	79

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	817	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B, D	protein	808	Homo sapiens	Q12879 (AlphaFold model)
008-218 Heavy	H, I	protein	220	Homo sapiens
008-218 Light	L, M	protein	209	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>8VUT_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
KIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLIS
SQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPY
SHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNV
TALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPD
GILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRV
LMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGG
ETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSP
GSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGE
LLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWL
LVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAP
RSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATV
KQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKC
DLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNA
PATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHK

Sequence of entity 2 (B, D), FASTA

>8VUT_2 Glutamate receptor ionotropic, NMDA 2A (chains B, D)
LNIAVMLGHSHDVTERELRTLWGPEQAAGLPLDVNVVALLMNRTDPKSLITHVCDLMSGA
RIHGLVFGDDTDQEAVAQMLDFISSHTFVPILGIHGGASMIMADKDPTSTFFQFGASIQQ
QATVMLKIMQDYDWHVFSLVTTIFPGYREFISFVKTTVDNSFVGWDMQNVITLDTSFEDA
KTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFP
SGLISVSYDDWDYSLEARVRDGIGILTTAASSMLEKFSYIPEAKASCYGQMERPEVPMHT
LHPFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENHTLSLRHAVWPRY
KSFSDCEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVK
KCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLT
INEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAV
FVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSV
WAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERN
IRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSG
YIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLD
IDNMAGVFYMLAAAMALSLITFIWEHLF

Sequence of entity 3 (H, I), FASTA

>8VUT_3 008-218 Heavy (chains H, I)
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQVPGKGLEWVSGISWSSGSIGY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCAKDRASSWYAYGMDVWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV

Sequence of entity 4 (L, M), FASTA

>8VUT_4 008-218 Light (chains L, M)
NFMLTQPHSVSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYDDNQRPSGVP
NRFSGSIDSSSNSASLIISGLKTEDEADYYCQSTRVFGGGTKLTVLGQPKAAPSVTLFPP
SSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSL
TPEQWKSHRSYSCQVTHEGSTVEKTVAPT

Primary citation

Structural and functional mechanisms of anti-NMDAR autoimmune encephalitis. Michalski, K., Abdulla, T., Kleeman, S. et al. Nat Struct Mol Biol (2024) 31:1975-1986. DOI 10.1038/s41594-024-01386-4 · 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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