7EU7: Human GluN1-GluN2A NMDA receptor

Structure of the human GluN1-GluN2A NMDA receptor in complex with S-ketamine, glycine and glutamate. Determined by electron microscopy at 3.5 Å resolution. Released 4 Aug 2021.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 21,773
Mol. weight: 384.74 kDa
Ligands: NAG, GLU, JC9, GLY
Released: 4 Aug 2021

Explore 7EU7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EU7 contains 132 α-helices and 162 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: 34 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	1
α-helix	36-52	17
β-strand	65-66	2	1
α-helix	71-81	11
α-helix	83-85	3
β-strand	90-92	3	1
α-helix	104-113	10
α-helix	116-117	2
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	147-157	11
β-strand	164-167	4	2
α-helix	171-184	14
β-strand	193-196	4	2
α-helix	205-212	8
β-strand	216	1	3
β-strand	218-222	5	2
α-helix	225-236	12
β-strand	246-249	4	2
α-helix	251-253	3
α-helix	257-261	5
α-helix	262-263	2
β-strand	266-271	6	2
α-helix	277-296	20
α-helix	302-305	4
α-helix	318-327	10
β-strand	330	1	4
β-strand	338	1	4
β-strand	339-340	2	5
β-strand	345	1	1
β-strand	346-347	2	5
β-strand	351-357	7	2
β-strand	360-367	8	2
β-strand	372-374	3	2
β-strand	392	1	3
β-strand	399-401	3	6
β-strand	405	1	7
β-strand	409-412	4	7
β-strand	424	1	8
α-helix	429	1
β-strand	430	1	8
α-helix	431-432	2
β-strand	434	1	7
β-strand	437-439	3	6
β-strand	450-452	3	6
β-strand	454-457	4	7
α-helix	458-470	13
β-strand	475-477	3	6
β-strand	487-489	3	9
α-helix	490	1
β-strand	496-498	3	9
α-helix	500-506	7
β-strand	512-513	2	6
β-strand	518	1	10
β-strand	527-528	2	11
β-strand	538-543	6	12
α-helix	545-547	3
α-helix	560-581	22
α-helix	603-613	11
α-helix	627-656	30
α-helix	666-668	3
α-helix	670-673	4
β-strand	681	1	13
β-strand	684	1	14
α-helix	688-694	7
α-helix	700-706	7
β-strand	711	1	14
α-helix	714-722	9
β-strand	728	1	13
β-strand	729-732	4	12
α-helix	733-742	10
β-strand	746-753	8	12
β-strand	758	1	10
β-strand	761	1	6
β-strand	762-763	2	11
α-helix	769-781	13
α-helix	784-792	9
α-helix	811-837	27

Chain B: 30 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	15
α-helix	48-54	7
β-strand	68-73	6	15
α-helix	79-91	13
α-helix	92-94	3
β-strand	98-101	4	15
α-helix	108-120	13
β-strand	124-126	3	15
α-helix	129-132	4
β-strand	144-146	3	15
α-helix	151-164	14
β-strand	171-175	5	16
α-helix	180-192	13
β-strand	204-206	3	16
α-helix	215-219	5
β-strand	226-230	5	16
α-helix	233-244	12
β-strand	254-257	4	16
α-helix	259-261	3
α-helix	273	1
β-strand	277-280	4	16
α-helix	288-309	22
α-helix	313-314	2
α-helix	335-339	5
β-strand	343	1	17
β-strand	346	1	17
β-strand	350	1	18
β-strand	356	1	18
β-strand	362-366	5	16
β-strand	372-377	6	16
β-strand	385	1	16
α-helix	400-401	2
β-strand	405-410	6	19
β-strand	418-420	3	19
α-helix	421-423	3
β-strand	434-441	8	19
β-strand	449-457	9	19
α-helix	459-471	13
β-strand	474-479	6	19
β-strand	488-489	2	20
β-strand	492-493	2	20
α-helix	495-501	7
β-strand	507-508	2	19
β-strand	523-524	2	19
β-strand	531	1	21
β-strand	533-538	6	22
α-helix	556-577	22
α-helix	600-613	14
α-helix	625-654	30
α-helix	668-671	4
β-strand	682-683	2	22
β-strand	684	1	23
α-helix	689-697	9
α-helix	699-706	8
β-strand	709	1	23
α-helix	713-721	9
β-strand	727-731	5	22
α-helix	732-740	9
β-strand	747-749	3	22
β-strand	759	1	21
β-strand	764-765	2	19
α-helix	772-784	13
α-helix	787-796	10
α-helix	799-802	4
α-helix	818-840	23

Chain C: 37 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	28-29	2	24
β-strand	30-33	4	25
α-helix	36-52	17
β-strand	61-62	2	24
β-strand	65-66	2	25
α-helix	71-77	7
α-helix	78-83	6
β-strand	90-92	3	25
α-helix	104-113	10
β-strand	118-120	3	25
α-helix	126-129	4
β-strand	137-139	3	25
α-helix	144-146	3
α-helix	147-158	12
β-strand	164-168	5	26
α-helix	171-186	16
β-strand	193-197	5	26
α-helix	205-212	8
β-strand	216	1	27
β-strand	218-220	3	26
α-helix	225-237	13
β-strand	246-249	4	26
α-helix	251-253	3
α-helix	257-261	5
α-helix	262-263	2
β-strand	266-271	6	26
α-helix	277-296	20
α-helix	302-305	4
α-helix	318-326	9
β-strand	330	1	28
β-strand	338	1	28
β-strand	339-340	2	29
β-strand	345	1	25
β-strand	346-347	2	29
β-strand	351-356	6	26
β-strand	361-367	7	26
β-strand	372-374	3	26
α-helix	382-384	3
β-strand	392	1	27
β-strand	399-402	4	30
β-strand	405	1	31
β-strand	409	1	31
β-strand	410-412	3	32
α-helix	413-415	3
β-strand	424	1	33
α-helix	429	1
β-strand	430	1	33
α-helix	431-432	2
β-strand	434-439	6	32
β-strand	450-456	7	32
α-helix	458-470	13
β-strand	475-478	4	30
β-strand	487-489	3	34
α-helix	490	1
β-strand	496-498	3	34
α-helix	500-506	7
β-strand	512-513	2	30
α-helix	521-524	4
β-strand	527	1	35
β-strand	538-543	6	36
α-helix	544-546	3
α-helix	561-579	19
α-helix	603-613	11
α-helix	627-657	31
α-helix	670-673	4
β-strand	676	1	37
β-strand	679	1	37
β-strand	681	1	38
β-strand	684	1	39
α-helix	688-694	7
α-helix	700-706	7
β-strand	711	1	39
α-helix	714-722	9
β-strand	728	1	38
β-strand	729-732	4	36
α-helix	733-742	10
β-strand	746-753	8	36
β-strand	761-762	2	30
β-strand	763	1	35
α-helix	769-782	14
α-helix	784-792	9
α-helix	810-815	6
α-helix	817-840	24

Chain D: 31 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	40
α-helix	46-54	9
α-helix	57-60	4
β-strand	68-73	6	40
α-helix	79-91	13
β-strand	97-100	4	40
α-helix	108-120	13
β-strand	124-126	3	40
α-helix	134-135	2
β-strand	144-145	2	40
α-helix	151-164	14
β-strand	169-170	2	41
β-strand	171-175	5	42
α-helix	180-193	14
β-strand	199-200	2	41
β-strand	204-206	3	42
α-helix	213-219	7
β-strand	226-230	5	42
α-helix	233-244	12
β-strand	254-257	4	42
α-helix	260-262	3
β-strand	277-280	4	42
α-helix	288-309	22
α-helix	313-314	2
α-helix	332-333	2
α-helix	335-339	5
β-strand	343	1	43
β-strand	346	1	43
β-strand	350	1	44
β-strand	356	1	44
β-strand	362-366	5	42
β-strand	372-377	6	42
β-strand	385	1	42
α-helix	399-401	3
β-strand	405-410	6	45
β-strand	414	1	46
β-strand	417	1	46
β-strand	418-420	3	47
α-helix	421-423	3
β-strand	434-439	6	47
β-strand	451-457	7	47
α-helix	459-471	13
β-strand	474-479	6	45
β-strand	487-489	3	48
β-strand	492-494	3	48
α-helix	496-501	6
β-strand	507-508	2	45
β-strand	531	1	49
β-strand	533-538	6	50
α-helix	557-577	21
α-helix	600-613	14
α-helix	625-651	27
α-helix	652-654	3
α-helix	668-671	4
β-strand	682-683	2	50
α-helix	689-697	9
α-helix	699-705	7
α-helix	706-708	3
α-helix	713-722	10
β-strand	727-731	5	50
α-helix	732-740	9
β-strand	747-749	3	50
β-strand	759	1	49
β-strand	764-765	2	45
α-helix	772-784	13
α-helix	787-795	9
α-helix	814-840	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	847	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B, D	protein	841	Homo sapiens	Q12879 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7EU7_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNM
TGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA
DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDARRKQ

Sequence of entity 2 (B, D), FASTA

>7EU7_2 Glutamate receptor ionotropic, NMDA 2A (chains B, D)
MGRVGYWTLLVLPALLVWRGPAPSAAAEKGPPALNIAVMLGHSHDVTERELRTLWGPEQA
AGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSHT
FVPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGY
REFISFVKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLIL
SEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGIGILT
TAASSMLEKFSYIPEAKASCYGQMERPEVPMHTLHPFMVNVTWDGKDLSFTEEGYQVHPR
LVVIVLNKDREWEKVGKWENHTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVE
DIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLV
TNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRS
NGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFT
IGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVD
QVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSL
KTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALL
QFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHL
F

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	24
GLU	Glutamic acid	C5 H9 N O4	2
JC9	(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one	C13 H16 Cl N O	1
GLY	Glycine	C2 H5 N O2	2

Primary citation

Structural basis of ketamine action on human NMDA receptors. Zhang, Y., Ye, F., Zhang, T. et al. Nature (2021) 596:301-305. DOI 10.1038/s41586-021-03769-9 · 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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