8VUR: Human GluN1-2A with IgG 003-102 WT conformation

Human GluN1-2A with IgG 003-102 WT conformation. Determined by electron microscopy at 3.84 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.84 Å
Organism: Homo sapiens
Chains: 6
Atoms: 24,978
Mol. weight: 413.47 kDa
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8VUR contains 125 α-helices and 204 β-strands across 6 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: 28 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	1
β-strand	33	1	2
α-helix	37-52	16
β-strand	66	1	2
α-helix	72-81	10
α-helix	83-85	3
β-strand	90-92	3	1
α-helix	104-113	10
β-strand	118-120	3	1
β-strand	138-139	2	1
α-helix	145-158	14
β-strand	167	1	3
α-helix	171-185	15
β-strand	196	1	3
α-helix	205-210	6
β-strand	216	1	4
β-strand	218-219	2	5
α-helix	225-236	12
β-strand	246-247	2	5
β-strand	249	1	6
α-helix	252-254	3
β-strand	268	1	6
β-strand	271	1	7
α-helix	278-295	18
α-helix	318-326	9
β-strand	329-330	2	8
β-strand	338-339	2	8
β-strand	351	1	7
β-strand	354-357	4	9
β-strand	360-363	4	9
β-strand	365-367	3	7
β-strand	372-374	3	7
β-strand	392	1	4
β-strand	397-398	2	10
β-strand	400	1	11
β-strand	401-402	2	12
β-strand	405	1	13
β-strand	409	1	13
β-strand	412	1	14
α-helix	413-415	3
β-strand	434-436	3	14
β-strand	453-455	3	14
α-helix	458-470	13
β-strand	473-474	2	10
β-strand	477-478	2	12
β-strand	488-489	2	15
β-strand	496-497	2	15
α-helix	500-506	7
β-strand	512	1	11
α-helix	521-524	4
β-strand	528	1	16
β-strand	538-539	2	17
β-strand	542-543	2	18
α-helix	560-579	20
α-helix	584-595	12
α-helix	608-637	30
α-helix	651-654	4
β-strand	662	1	19
α-helix	669-676	8
α-helix	681-688	8
α-helix	695-703	9
β-strand	709	1	19
β-strand	712-713	2	17
α-helix	714-723	10
β-strand	727-728	2	18
β-strand	734	1	17
β-strand	743	1	16
α-helix	750-763	14
α-helix	765-769	5
α-helix	770-774	5
α-helix	783-796	14
α-helix	799-812	14

Chain B: 28 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	20
β-strand	38	1	21
β-strand	39-40	2	22
α-helix	49-53	5
β-strand	68	1	20
β-strand	72-73	2	22
α-helix	79-90	12
β-strand	99	1	21
α-helix	109-119	11
β-strand	124-125	2	23
α-helix	129-132	4
α-helix	134-135	2
β-strand	144-145	2	23
α-helix	151-164	14
β-strand	170	1	24
β-strand	173-175	3	25
α-helix	180-191	12
β-strand	200	1	24
β-strand	204-206	3	25
α-helix	214-220	7
β-strand	226-227	2	26
β-strand	230	1	25
α-helix	233-244	12
β-strand	254-255	2	26
β-strand	256	1	27
β-strand	277-281	5	27
α-helix	288-310	23
α-helix	335-337	3
β-strand	343	1	28
β-strand	346	1	28
β-strand	350	1	29
β-strand	356	1	29
β-strand	361-365	5	27
β-strand	366	1	30
β-strand	372	1	30
β-strand	377-378	2	27
α-helix	400-402	3
β-strand	405-406	2	31
β-strand	409-410	2	32
β-strand	417-419	3	32
α-helix	421-423	3
β-strand	434-437	4	32
β-strand	453-458	6	32
α-helix	460-471	12
β-strand	474-475	2	31
β-strand	478-479	2	32
β-strand	486	1	33
β-strand	489	1	34
β-strand	492	1	34
β-strand	495	1	33
α-helix	496-501	6
β-strand	513	1	35
α-helix	516-521	6
β-strand	533-536	4	36
α-helix	548-550	3
α-helix	556-577	22
α-helix	580-593	14
α-helix	605-634	30
α-helix	649-651	3
β-strand	663	1	36
α-helix	670-677	8
α-helix	679-685	7
α-helix	694-702	9
β-strand	708-711	4	36
α-helix	712-720	9
β-strand	741	1	35
α-helix	752-765	14
α-helix	767-775	9
α-helix	791-813	23

Chain C: 36 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	37
α-helix	36-52	17
β-strand	64-65	2	37
α-helix	71-78	8
α-helix	79-83	5
β-strand	91-92	2	37
α-helix	105-113	9
β-strand	119-120	2	37
α-helix	126-129	4
β-strand	139	1	37
α-helix	144-156	13
β-strand	164-168	5	38
α-helix	171-184	14
α-helix	185-187	3
β-strand	193-197	5	38
α-helix	205-210	6
α-helix	226-237	12
β-strand	248-249	2	39
α-helix	251-253	3
α-helix	257-260	4
β-strand	267-268	2	39
β-strand	270-271	2	40
α-helix	278-295	18
α-helix	303-305	3
α-helix	314-315	2
α-helix	318-326	9
β-strand	330	1	41
β-strand	338	1	41
β-strand	339-340	2	42
β-strand	346-347	2	42
β-strand	351-356	6	40
β-strand	361-367	7	40
β-strand	372-374	3	40
α-helix	388-390	3
β-strand	398	1	43
β-strand	401-402	2	44
β-strand	409	1	45
β-strand	412	1	46
α-helix	413-415	3
β-strand	434-437	4	46
β-strand	452-455	4	46
β-strand	457	1	45
α-helix	458-469	12
β-strand	474	1	43
β-strand	477-478	2	44
β-strand	487-489	3	47
α-helix	490	1
β-strand	496-498	3	47
α-helix	500-505	6
β-strand	518	1	48
α-helix	521-526	6
β-strand	541-543	3	49
α-helix	544-546	3
α-helix	560-565	6
α-helix	569-579	11
α-helix	584-594	11
α-helix	608-637	30
α-helix	651-654	4
α-helix	671-676	6
α-helix	678-682	5
α-helix	685-688	4
α-helix	697-703	7
α-helix	714-723	10
β-strand	727-729	3	49
β-strand	739	1	48
α-helix	750-762	13
α-helix	765-773	9
α-helix	782-812	31

Chain D: 29 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	38	1	50
α-helix	50-53	4
β-strand	71	1	50
α-helix	79-92	14
α-helix	108-118	11
β-strand	124-125	2	51
α-helix	129-132	4
β-strand	144-145	2	51
α-helix	151-164	14
β-strand	170	1	52
β-strand	174	1	53
α-helix	180-192	13
β-strand	200	1	52
α-helix	213-220	8
β-strand	226-227	2	54
β-strand	230	1	53
α-helix	234-246	13
β-strand	254-255	2	54
α-helix	273	1
β-strand	280	1	55
α-helix	288-310	23
α-helix	335-337	3
β-strand	350-351	2	56
β-strand	353-356	4	56
β-strand	362	1	55
β-strand	366	1	57
β-strand	372	1	57
β-strand	377	1	55
α-helix	399-401	3
β-strand	406	1	58
β-strand	408	1	59
β-strand	409-410	2	60
β-strand	413	1	61
β-strand	417-419	3	61
α-helix	421-423	3
β-strand	434	1	61
β-strand	437-439	3	60
α-helix	444-446	3
β-strand	451-453	3	60
β-strand	456-458	3	61
α-helix	460-471	12
β-strand	475	1	58
β-strand	478-479	2	60
β-strand	487-489	3	62
β-strand	492-494	3	62
α-helix	497-501	5
β-strand	507	1	59
β-strand	513	1	63
α-helix	517-521	5
β-strand	533-538	6	64
α-helix	557-577	21
α-helix	580-593	14
α-helix	605-632	28
α-helix	648-651	4
β-strand	663	1	64
α-helix	669-677	9
α-helix	681-684	4
α-helix	686-688	3
α-helix	693-701	9
β-strand	708-711	4	64
α-helix	712-720	9
β-strand	727-729	3	64
β-strand	741	1	63
α-helix	752-764	13
α-helix	767-775	9
α-helix	787-813	27

Chain H: 2 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	65
β-strand	16	1	66
β-strand	19-24	6	65
β-strand	33-36	4	67
β-strand	39-40	2	68
β-strand	47	1	68
β-strand	51-52	2	67
β-strand	58	1	67
α-helix	65-67	3
β-strand	68-73	6	65
β-strand	78-83	6	65
β-strand	86	1	66
α-helix	88-90	3
β-strand	93-94	2	68
β-strand	97-100	4	67
β-strand	107-110	4	67
β-strand	114	1	68
β-strand	232-236	5	69
β-strand	247-248	2	70
β-strand	250-254	5	69
β-strand	265-269	5	71
β-strand	276-281	6	71
β-strand	287-288	2	71
β-strand	299-302	4	69
β-strand	307-310	4	69
β-strand	311-312	2	70
β-strand	322-326	5	71
β-strand	339	1	71
β-strand	343	1	71

Chain L: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	72
β-strand	10-11	2	73
β-strand	19-24	6	72
β-strand	34-39	6	74
β-strand	46-49	4	74
β-strand	64-67	4	72
β-strand	73-77	5	72
α-helix	83-85	3
β-strand	88-94	7	74
β-strand	99-101	3	74
β-strand	102	1	72
β-strand	107-108	2	73
β-strand	233-234	2	75
β-strand	238-240	3	76
β-strand	246-253	8	75
β-strand	264-268	5	76
β-strand	275-278	4	76
β-strand	279	1	77
β-strand	283	1	77
β-strand	292-296	5	75
β-strand	302-308	7	75
α-helix	312-314	3
β-strand	317-323	7	76
β-strand	328-330	3	76
β-strand	334-337	4	76

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A	protein	815	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B, D	protein	808	Homo sapiens	Q12879 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 1	C	protein	815	Homo sapiens	Q05586 (AlphaFold model)
003-102 Heavy	H	protein	234	Homo sapiens
003-102 Light	L	protein	218	Homo sapiens

Sequence of entity 1 (A), FASTA

>8VUR_1 Glutamate receptor ionotropic, NMDA 1 (chains A)
VNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQ
VYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSH
QSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTA
LLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGI
LGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLM
SSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGET
EKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGS
PRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELL
SGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLV
GLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRS
FSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQ
SSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDL
VTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPA
TLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHK

Sequence of entity 2 (B, D), FASTA

>8VUR_2 Glutamate receptor ionotropic, NMDA 2A (chains B, D)
LNIAVMLGHSHDVTERELRTLWGPEQAAGLPLDVNVVALLMNRTDPKSLITHVCDLMSGA
RIHGLVFGDDTDQEAVAQMLDFISSHTFVPILGIHGGASMIMADKDPTSTFFQFGASIQQ
QATVMLKIMQDYDWHVFSLVTTIFPGYREFISFVKTTVDNSFVGWDMQNVITLDTSFEDA
KTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFP
SGLISVSYDDWDYSLEARVRDGIGILTTAASSMLEKFSYIPEAKASCYGQMERPEVPMHT
LHPFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENHTLSLRHAVWPRY
KSFSDCEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVK
KCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLT
INEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAV
FVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSV
WAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERN
IRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSG
YIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLD
IDNMAGVFYMLAAAMALSLITFIWEHLF

Sequence of entity 3 (C), FASTA

>8VUR_3 Glutamate receptor ionotropic, NMDA 1 (chains C)
VNIGAVLSTRKHEQMFREAVNQANKRHASWKIQLNATSVTHKPNAIQMALSVCEDLISSQ
VYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSH
QSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTA
LLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGI
LGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLM
SSKYADGVTGRVEFNEDGDRKFANYSIMNLQRRKLVQVGIYNGTHVIPNDRKIIWPGGET
EKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGS
PRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELL
SGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLV
GLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRS
FSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQ
SSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDL
VTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPA
TLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHK

Sequence of entity 4 (H), FASTA

>8VUR_4 003-102 Heavy (chains H)
LQLQESGPGLVKPSQTLSLTCTVSGGSISSSNWWSWVRQPPGKGLEWIGEIYHSGNTNYN
PSLKSRVTVSVDKSKNQFSLKLTSVTAADTAVYYCARDVSGGVNWFDPWGQGTLVTVLQL
QESGPGLVKPSQTLSLTCTVSGGSISSSNWWSWVRQPPGKGLEWIGEIYHSGNTNYNPSL
KSRVTVSVDKSKNQFSLKLTSVTAADTAVYYCARDVSGGVNWFDPWGQGTLVTV

Sequence of entity 5 (L), FASTA

>8VUR_5 003-102 Light (chains L)
NFMLTQPHSVSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSAPTTVIYEDNQRPSGVP
DRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSTVVFGGGTKLTVNFMLTQPHSVS
ESPGKTVTISCTRSSGSIASNYVQWYQQRPGSAPTTVIYEDNQRPSGVPDRFSGSIDSSS
NSASLTISGLKTEDEADYYCQSYDSSTVVFGGGTKLTV

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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