8JJ1: GluN1-2A NMDAR

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in two fab conformation. Determined by electron microscopy at 3.77 Å resolution. Released 5 Jun 2024.

Method: Electron microscopy
Resolution: 3.77 Å
Organism: Homo sapiens
Chains: 8
Atoms: 28,026
Mol. weight: 486.92 kDa
Ligands: NAG
Released: 5 Jun 2024

Explore 8JJ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JJ1 contains 143 α-helices and 191 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: 33 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	3
α-helix	46-58	13
β-strand	68-73	6	3
α-helix	79-90	12
β-strand	97-100	4	3
α-helix	108-120	13
β-strand	124-126	3	3
α-helix	130-132	3
α-helix	137-139	3
β-strand	144-146	3	3
α-helix	151-164	14
β-strand	169-170	2	4
β-strand	172-175	4	5
α-helix	180-192	13
β-strand	199-200	2	4
α-helix	202-203	2
β-strand	204-206	3	5
α-helix	215-220	6
β-strand	226-230	5	5
α-helix	233-246	14
β-strand	254-257	4	5
α-helix	273	1
β-strand	277-280	4	5
α-helix	288-309	22
α-helix	312-314	3
α-helix	335-338	4
β-strand	343	1	6
β-strand	346	1	6
β-strand	350	1	7
β-strand	356	1	7
β-strand	362-367	6	5
β-strand	371-377	7	5
α-helix	380-382	3
β-strand	385-386	2	5
β-strand	407-410	4	8
β-strand	418-420	3	9
α-helix	421-423	3
β-strand	434-439	6	9
β-strand	443	1	10
β-strand	446	1	10
β-strand	451-457	7	9
α-helix	459-471	13
β-strand	476-479	4	8
β-strand	489	1	11
β-strand	492	1	11
α-helix	495-501	7
β-strand	507-508	2	8
α-helix	512-514	3
α-helix	516-519	4
β-strand	523-524	2	8
β-strand	530-531	2	12
β-strand	533-538	6	13
α-helix	560-578	19
α-helix	604-609	6
α-helix	626-650	25
α-helix	668-671	4
β-strand	684	1	14
α-helix	690-697	8
α-helix	699-705	7
α-helix	706-708	3
β-strand	709	1	14
α-helix	713-721	9
β-strand	727-731	5	13
α-helix	732-741	10
α-helix	743-745	3
β-strand	747-749	3	13
β-strand	759-760	2	12
β-strand	764-765	2	8
α-helix	772-784	13
α-helix	789-795	7
α-helix	814-836	23

Chain B: 34 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	27-33	7	15
α-helix	36-50	15
β-strand	60-66	7	15
α-helix	71-81	11
α-helix	83-85	3
β-strand	87-92	6	15
α-helix	105-113	9
β-strand	118-120	3	15
α-helix	126-129	4
β-strand	137-139	3	15
α-helix	144-146	3
α-helix	147-158	12
β-strand	164-168	5	16
α-helix	171-184	14
α-helix	185-187	3
β-strand	193-197	5	16
α-helix	205-212	8
β-strand	218-222	5	16
α-helix	225-237	13
β-strand	246-249	4	16
α-helix	257-260	4
α-helix	262-263	2
β-strand	267-271	5	16
α-helix	277-298	22
α-helix	313-315	3
α-helix	318-326	9
β-strand	330	1	17
β-strand	338	1	17
β-strand	340	1	18
β-strand	346	1	18
β-strand	351-357	7	16
β-strand	360-367	8	16
β-strand	372-374	3	16
α-helix	380-381	2
β-strand	397-402	6	19
β-strand	405	1	20
β-strand	409	1	20
β-strand	410-413	4	19
β-strand	424	1	21
α-helix	429	1
β-strand	430	1	21
α-helix	431-432	2
β-strand	434-439	6	19
β-strand	450-456	7	19
α-helix	458-470	13
β-strand	473-478	6	19
β-strand	487	1	22
β-strand	498	1	22
α-helix	500-506	7
β-strand	512-513	2	19
β-strand	518	1	23
α-helix	521-524	4
β-strand	528-529	2	19
β-strand	534-536	3	23
β-strand	538-543	6	24
α-helix	561-581	21
α-helix	605-614	10
α-helix	627-655	29
α-helix	661-663	3
α-helix	670-673	4
β-strand	676	1	25
β-strand	679	1	25
β-strand	681-682	2	24
α-helix	688-695	8
α-helix	700-706	7
α-helix	714-722	9
β-strand	728-732	5	24
α-helix	733-742	10
β-strand	746-749	4	24
β-strand	756-758	3	23
β-strand	761-762	2	19
α-helix	769-782	14
α-helix	784-792	9
α-helix	812-839	28

Chain C: 35 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	26
α-helix	46-54	9
α-helix	57-59	3
α-helix	66-67	2
β-strand	68-73	6	26
α-helix	79-91	13
β-strand	97-100	4	26
α-helix	108-120	13
β-strand	124-126	3	26
α-helix	130-132	3
α-helix	137-139	3
β-strand	144-146	3	26
α-helix	151-164	14
β-strand	169	1	27
β-strand	172-175	4	28
α-helix	180-193	14
β-strand	199	1	27
α-helix	202-203	2
β-strand	204-206	3	28
α-helix	215-219	5
β-strand	226-230	5	28
α-helix	233-244	12
β-strand	254-257	4	28
α-helix	273	1
β-strand	277-280	4	28
α-helix	288-309	22
α-helix	313-314	2
α-helix	336-338	3
β-strand	343	1	29
β-strand	346	1	29
β-strand	350	1	30
β-strand	356	1	30
β-strand	362-366	5	28
β-strand	372-377	6	28
β-strand	385-386	2	28
β-strand	406-410	5	31
β-strand	420	1	31
α-helix	421-423	3
β-strand	434-443	10	31
β-strand	446-456	11	31
α-helix	459-471	13
β-strand	475-479	5	31
β-strand	489	1	32
β-strand	492	1	32
α-helix	495-501	7
β-strand	507-508	2	31
α-helix	516-519	4
β-strand	523-524	2	31
β-strand	530-531	2	33
β-strand	533-538	6	34
α-helix	561-578	18
α-helix	600-604	5
α-helix	605-612	8
α-helix	626-631	6
α-helix	634-652	19
α-helix	668-671	4
α-helix	673-675	3
β-strand	682-683	2	34
α-helix	689-695	7
α-helix	699-705	7
α-helix	706-708	3
α-helix	713-722	10
β-strand	727-731	5	34
α-helix	732-741	10
β-strand	747-749	3	34
β-strand	759-760	2	33
β-strand	764-765	2	31
α-helix	772-784	13
α-helix	789-795	7
α-helix	814-836	23

Chain D: 32 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	35
α-helix	36-50	15
β-strand	61-66	6	35
α-helix	71-81	11
α-helix	83-85	3
β-strand	87-92	6	35
α-helix	105-113	9
β-strand	118-120	3	35
β-strand	137-139	3	35
α-helix	147-158	12
β-strand	164-168	5	36
α-helix	171-184	14
α-helix	185-187	3
β-strand	194-197	4	36
α-helix	205-212	8
β-strand	218-222	5	36
α-helix	225-237	13
β-strand	246-249	4	36
α-helix	257-260	4
α-helix	262-263	2
β-strand	266-271	6	36
α-helix	277-298	22
α-helix	303-305	3
α-helix	318-327	10
β-strand	329-330	2	37
β-strand	338-339	2	37
β-strand	340	1	38
β-strand	346	1	38
β-strand	351-357	7	36
β-strand	360-367	8	36
β-strand	372-374	3	36
α-helix	388-389	2
β-strand	397-402	6	39
β-strand	409-412	4	39
β-strand	424	1	40
α-helix	429	1
β-strand	430	1	40
α-helix	431-432	2
β-strand	434-437	4	39
β-strand	452-457	6	39
α-helix	458-470	13
β-strand	473-478	6	39
β-strand	488	1	41
β-strand	497	1	41
α-helix	500-506	7
β-strand	512-516	5	39
α-helix	521-524	4
β-strand	528-529	2	39
β-strand	538-543	6	42
α-helix	561-582	22
α-helix	605-614	10
α-helix	627-653	27
α-helix	654-658	5
α-helix	670-673	4
β-strand	676	1	43
β-strand	679	1	43
β-strand	681-682	2	42
α-helix	688-695	8
α-helix	700-706	7
α-helix	714-722	9
β-strand	728-732	5	42
α-helix	733-742	10
β-strand	746-753	8	42
β-strand	759-762	4	39
α-helix	770-781	12
α-helix	784-792	9
α-helix	811-836	26

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	44
α-helix	7-9	3
β-strand	10-12	3	45
β-strand	18-25	8	44
β-strand	32-39	8	45
β-strand	45-51	7	45
β-strand	58-60	3	45
β-strand	68-73	6	44
β-strand	78-83	6	44
α-helix	88-90	3
β-strand	92-100	9	45
β-strand	110-111	2	45
β-strand	115-119	5	45

Chain F: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	46
β-strand	10-13	4	47
β-strand	19-25	7	46
β-strand	33-38	6	47
β-strand	45-49	5	47
β-strand	53-54	2	47
α-helix	55	1
β-strand	62-67	6	46
β-strand	70-75	6	46
α-helix	80-82	3
β-strand	85-90	6	47
β-strand	100-104	5	47

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	48
β-strand	10-13	4	49
β-strand	19-25	7	48
β-strand	33-38	6	49
β-strand	45-49	5	49
β-strand	53-54	2	49
α-helix	55	1
β-strand	62-67	6	48
β-strand	70-75	6	48
α-helix	80-82	3
β-strand	85-90	6	49
α-helix	91-93	3
β-strand	96	1	49
β-strand	100-104	5	49

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	32-39	8	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	111	1	2
β-strand	115-119	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 2G7 Heavy Chain	E, H	protein	253	Homo sapiens
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)
Fab 2G7 Light Chain	F, G	protein	234	Homo sapiens

Sequence of entity 1 (E, H), FASTA

>8JJ1_1 Fab 2G7 Heavy Chain (chains E, H)
MDWTWSILFLVAAPTGAHSQVQLVQSGAEVRKPGASVKVSCRASGYSFTGYYVHWVRQAP
GQGLEWLGWINPNTGGTDYSQKFQGRVTMTRDTSITTAYVELSSLISDDTAVYYCARDAT
GAASSPFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS
WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP
KSCDKTHTCPPCP

Sequence of entity 2 (A, C), FASTA

>8JJ1_2 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 3 (B, D), FASTA

>8JJ1_3 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 4 (F, G), FASTA

>8JJ1_4 Fab 2G7 Light Chain (chains F, G)
MDMRVPAQLLGLLLLWLRGARCDIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQ
RPGQAPKLLIYMASTLQTGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQHYKSYSFGP
GTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

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

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