7EOT: Glutamate receptor ionotropic, NMDA 2A

Structure of the human GluN1/GluN2A NMDA receptor in the CGP-78608/glutamate bound state. Determined by electron microscopy at 3.8 Å resolution. Released 30 Jun 2021.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,598
Mol. weight: 385.79 kDa
Ligands: J86, NAG
Released: 30 Jun 2021

Explore 7EOT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EOT contains 128 α-helices and 150 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: 29 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
α-helix	46-55	10
β-strand	68-73	6	1
α-helix	79-90	12
β-strand	97-100	4	1
α-helix	108-120	13
β-strand	124-126	3	1
α-helix	137-139	3
β-strand	144	1	1
α-helix	151-165	15
β-strand	169-170	2	2
β-strand	172-175	4	3
α-helix	180-193	14
β-strand	199-200	2	2
α-helix	201-203	3
β-strand	204-206	3	3
α-helix	214-219	6
β-strand	226-230	5	3
α-helix	233-245	13
β-strand	254-257	4	3
β-strand	276-280	5	3
α-helix	288-309	22
α-helix	332-333	2
α-helix	336-338	3
β-strand	342-343	2	4
β-strand	346-347	2	4
β-strand	350	1	5
β-strand	356	1	5
β-strand	362-366	5	3
β-strand	372-377	6	3
β-strand	385-386	2	3
β-strand	406-410	5	6
β-strand	435-441	7	6
β-strand	449-455	7	6
α-helix	459-471	13
β-strand	475-479	5	6
β-strand	489	1	7
β-strand	492	1	7
α-helix	495-500	6
β-strand	507-508	2	6
α-helix	512-514	3
β-strand	524	1	6
β-strand	531	1	8
β-strand	533-536	4	9
β-strand	537-538	2	10
α-helix	561-578	18
α-helix	603-612	10
α-helix	626-631	6
α-helix	634-651	18
α-helix	668-671	4
α-helix	673-675	3
α-helix	679-680	2
α-helix	689-697	9
α-helix	699-705	7
α-helix	713-722	10
β-strand	728-731	4	9
α-helix	732-740	9
β-strand	747-748	2	10
β-strand	759	1	8
β-strand	764	1	6
α-helix	772-785	14
α-helix	789-795	7
α-helix	814-836	23

Chain B: 33 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	11
α-helix	36-50	15
β-strand	65-66	2	11
α-helix	72-78	7
α-helix	79-83	5
β-strand	90-92	3	11
α-helix	105-111	7
β-strand	118-120	3	11
α-helix	126-128	3
β-strand	137-139	3	11
α-helix	144-146	3
α-helix	147-158	12
β-strand	164-168	5	12
α-helix	171-184	14
α-helix	185-187	3
β-strand	194-197	4	12
α-helix	205-212	8
β-strand	218-222	5	12
α-helix	225-237	13
β-strand	246-249	4	12
α-helix	258-261	4
β-strand	266-267	2	12
β-strand	269-271	3	13
α-helix	277-296	20
α-helix	303-305	3
α-helix	318-326	9
β-strand	330-333	4	14
β-strand	336-338	3	14
β-strand	339-340	2	15
β-strand	346-347	2	15
β-strand	351-357	7	13
β-strand	360-367	8	13
β-strand	372-373	2	13
β-strand	381	1	16
β-strand	385	1	16
β-strand	399-402	4	17
β-strand	412-413	2	18
α-helix	420-422	3
β-strand	424	1	19
α-helix	429	1
β-strand	430	1	19
α-helix	431-432	2
β-strand	434-437	4	18
β-strand	452-455	4	18
α-helix	458-470	13
β-strand	475-478	4	17
β-strand	487	1	20
β-strand	498	1	20
α-helix	500-506	7
β-strand	512	1	17
β-strand	513-516	4	21
α-helix	521-526	6
β-strand	528-529	2	21
β-strand	535	1	22
β-strand	539-543	5	23
α-helix	561-581	21
α-helix	605-614	10
α-helix	627-656	30
α-helix	670-673	4
β-strand	676	1	24
β-strand	679	1	24
β-strand	681-682	2	23
α-helix	688-695	8
α-helix	697-699	3
α-helix	700-706	7
α-helix	714-722	9
β-strand	728-731	4	23
α-helix	733-742	10
β-strand	746-749	4	23
β-strand	757	1	22
β-strand	759-762	4	21
α-helix	769-781	13
α-helix	784-792	9
α-helix	811-842	32

Chain C: 31 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	25
α-helix	46-55	10
β-strand	68-73	6	25
α-helix	79-90	12
β-strand	97-100	4	25
α-helix	108-120	13
β-strand	124-126	3	25
α-helix	137-139	3
β-strand	144	1	25
α-helix	149-150	2
α-helix	151-165	15
β-strand	172-175	4	26
α-helix	180-193	14
α-helix	201-203	3
β-strand	204-206	3	26
α-helix	214-219	6
β-strand	226-230	5	26
α-helix	233-245	13
β-strand	254-257	4	26
β-strand	276-280	5	26
α-helix	288-309	22
α-helix	332-333	2
α-helix	336-338	3
β-strand	342-343	2	27
β-strand	346-347	2	27
β-strand	350	1	28
β-strand	356	1	28
β-strand	362-366	5	26
β-strand	372-377	6	26
β-strand	385-386	2	26
β-strand	406-410	5	29
β-strand	417	1	30
β-strand	420	1	31
β-strand	434-439	6	31
β-strand	451-456	6	31
β-strand	458	1	30
α-helix	459-471	13
β-strand	475-479	5	29
β-strand	489	1	32
β-strand	492	1	32
α-helix	495-500	6
β-strand	507-508	2	29
α-helix	512-514	3
β-strand	523-524	2	29
β-strand	531	1	33
β-strand	533-538	6	34
α-helix	561-578	18
α-helix	603-612	10
α-helix	626-631	6
α-helix	632-634	3
α-helix	635-651	17
α-helix	668-671	4
α-helix	673-675	3
α-helix	679-680	2
α-helix	689-695	7
α-helix	699-705	7
α-helix	713-722	10
β-strand	727-731	5	34
α-helix	732-740	9
β-strand	747-748	2	34
β-strand	759	1	33
β-strand	764-765	2	29
α-helix	772-785	14
α-helix	789-795	7
α-helix	814-836	23

Chain D: 35 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	35
α-helix	36-50	15
α-helix	60-62	3
β-strand	65-66	2	35
α-helix	72-78	7
α-helix	79-83	5
β-strand	90-92	3	35
α-helix	105-111	7
β-strand	118-120	3	35
α-helix	126-128	3
β-strand	137-139	3	35
α-helix	144-146	3
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	258-261	4
β-strand	266-267	2	36
β-strand	269-271	3	37
α-helix	277-296	20
α-helix	303-305	3
α-helix	318-326	9
β-strand	333	1	38
β-strand	336	1	38
β-strand	339-340	2	39
β-strand	346-347	2	39
β-strand	351-357	7	37
β-strand	360-367	8	37
β-strand	372-373	2	37
β-strand	381	1	40
β-strand	385	1	40
β-strand	400-402	3	41
β-strand	410-413	4	42
α-helix	420-422	3
β-strand	424	1	43
α-helix	429	1
β-strand	430	1	43
α-helix	431-432	2
β-strand	434-439	6	42
β-strand	450-456	7	42
α-helix	458-470	13
β-strand	476-478	3	41
β-strand	487	1	44
β-strand	498	1	44
α-helix	500-506	7
β-strand	512	1	41
β-strand	513-516	4	45
α-helix	517-519	3
α-helix	521-526	6
β-strand	528-529	2	45
β-strand	535	1	46
β-strand	538-543	6	47
α-helix	561-581	21
α-helix	605-614	10
α-helix	627-656	30
α-helix	670-673	4
β-strand	676	1	48
β-strand	679	1	48
β-strand	681-682	2	47
α-helix	688-695	8
α-helix	697-699	3
α-helix	700-706	7
α-helix	714-722	9
β-strand	728-732	5	47
α-helix	733-742	10
β-strand	746-749	4	47
β-strand	757	1	46
β-strand	759-762	4	45
α-helix	769-781	13
α-helix	784-792	9
α-helix	811-842	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 2A	A, C	protein	853	Homo sapiens	Q12879 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 1	B, D	protein	847	Homo sapiens	Q05586 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7EOT_1 Glutamate receptor ionotropic, NMDA 2A (chains A, C)
MGRVGYWTLLVLPALLVWRGPAPSAAAEKGPPALNIAVMLGHSHDVTERELRTLWGPEQA
AGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSHT
FVPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGY
REFISFVKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLIL
SEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGIGILT
TAASSMLEKFSYIPEAKASCYGQMERPEVPMHTLHPFMVNVTWDGKDLSFTEEGYQVHPR
LVVIVLNKDREWEKVGKWENHTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVE
DIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLV
TNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRS
NGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFT
IGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVD
QVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSL
KTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALL
QFVGDGEMEELETCWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHL
FYKSRAEAKRMKG

Sequence of entity 2 (B, D), FASTA

>7EOT_2 Glutamate receptor ionotropic, NMDA 1 (chains B, D)
MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNM
TGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA
DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVCLSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDARRKQ

Ligands and cofactors

ID	Name	Formula	Copies
J86	[(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylam…	C11 H13 Br N3 O5 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16

Primary citation

Gating mechanism and a modulatory niche of human GluN1-GluN2A NMDA receptors. Wang, H., Lv, S., Stroebel, D. et al. Neuron (2021) 109:2443-2456.e5. DOI 10.1016/j.neuron.2021.05.031 · 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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