9OOQ: Glutamate receptor ionotropic, NMDA 1

Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR. Determined by electron microscopy at 3.2 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,897
Mol. weight: 386.42 kDa
Ligands: A1CE1, GLU, POV, GLY
Released: 29 Oct 2025

Explore 9OOQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OOQ contains 149 α-helices and 177 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: 36 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	27-28	2	1
β-strand	31-32	2	2
α-helix	36-50	15
β-strand	60-61	2	1
β-strand	65	1	2
α-helix	74-80	7
α-helix	82-85	4
β-strand	90-92	3	2
α-helix	104-113	10
β-strand	118-120	3	2
α-helix	127-129	3
β-strand	138-139	2	2
α-helix	144-147	4
α-helix	148-158	11
β-strand	163-165	3	3
β-strand	168	1	4
α-helix	171-186	16
β-strand	193	1	3
β-strand	197	1	4
α-helix	207-213	7
β-strand	216	1	5
β-strand	218-221	4	3
α-helix	225-237	13
β-strand	246-249	4	3
α-helix	251-253	3
α-helix	256-258	3
β-strand	267-268	2	3
β-strand	269-271	3	6
α-helix	277-294	18
α-helix	303-305	3
α-helix	317-327	11
β-strand	330	1	7
β-strand	338	1	7
β-strand	340	1	8
β-strand	346	1	8
β-strand	351-357	7	6
β-strand	360-367	8	6
β-strand	372-374	3	6
α-helix	382-384	3
α-helix	388-389	2
β-strand	392	1	5
β-strand	398-402	5	9
β-strand	405	1	10
β-strand	409	1	10
β-strand	410-413	4	11
α-helix	420-422	3
β-strand	424	1	12
β-strand	430	1	12
β-strand	434-436	3	11
β-strand	453-456	4	11
α-helix	458-470	13
β-strand	474-478	5	9
β-strand	486-488	3	13
β-strand	497-499	3	13
α-helix	501-505	5
β-strand	512-518	7	9
α-helix	521-526	6
β-strand	527-528	2	14
β-strand	534	1	9
β-strand	538-543	6	15
α-helix	560-582	23
α-helix	600-602	3
α-helix	603-615	13
α-helix	629-657	29
α-helix	670-673	4
β-strand	676	1	16
β-strand	679	1	16
β-strand	681-682	2	15
β-strand	684	1	17
α-helix	688-695	8
α-helix	700-707	8
β-strand	711	1	17
α-helix	714-722	9
β-strand	728-732	5	15
α-helix	733-742	10
β-strand	746-753	8	15
β-strand	758-761	4	9
β-strand	762-763	2	14
α-helix	769-781	13
α-helix	784-792	9
α-helix	799-801	3
α-helix	804-808	5
α-helix	812-814	3
α-helix	815-840	26

Chain B: 38 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-42	8	18
α-helix	47-56	10
β-strand	66-73	8	18
α-helix	78-92	15
β-strand	96-100	5	18
α-helix	107-119	13
β-strand	123-127	5	18
α-helix	133-134	2
β-strand	143-145	3	18
α-helix	150-163	14
β-strand	168-169	2	19
β-strand	171-173	3	20
α-helix	179-191	13
β-strand	198-199	2	19
β-strand	204	1	20
α-helix	213-219	7
β-strand	227-231	5	20
α-helix	234-247	14
β-strand	255-258	4	20
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	20
α-helix	289-310	22
α-helix	324-329	6
α-helix	333-340	8
β-strand	344	1	21
β-strand	347	1	21
β-strand	351	1	22
β-strand	357	1	22
β-strand	362-367	6	20
β-strand	373-375	3	20
β-strand	379-380	2	23
β-strand	383-384	2	23
β-strand	405-410	6	24
β-strand	413	1	25
β-strand	417	1	25
β-strand	418-420	3	26
α-helix	421-423	3
α-helix	429-430	2
β-strand	434-436	3	26
β-strand	437	1	24
β-strand	439	1	27
β-strand	452	1	27
β-strand	455-458	4	26
α-helix	460-472	13
β-strand	475-480	6	24
β-strand	488-490	3	28
β-strand	493-495	3	28
α-helix	497-502	6
β-strand	508	1	24
β-strand	514	1	29
α-helix	517-520	4
β-strand	524-525	2	30
β-strand	530-539	10	29
α-helix	540-541	2
β-strand	554	1	31
α-helix	556-560	5
α-helix	561-566	6
α-helix	567-579	13
α-helix	602-613	12
α-helix	627-655	29
α-helix	669-672	4
β-strand	683-684	2	29
α-helix	691-698	8
α-helix	700-706	7
α-helix	707-709	3
α-helix	714-723	10
β-strand	728-732	5	29
α-helix	733-742	10
α-helix	744-746	3
β-strand	748-750	3	29
β-strand	757-762	6	29
β-strand	765-766	2	30
α-helix	767	1
α-helix	773-786	14
α-helix	788-792	5
α-helix	793-797	5
α-helix	800-803	4
α-helix	816-818	3
α-helix	819-841	23

Chain C: 37 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	32
β-strand	32	1	33
α-helix	36-51	16
β-strand	59-61	3	32
β-strand	65	1	33
α-helix	72-85	14
β-strand	90-92	3	33
α-helix	105-111	7
β-strand	118-120	3	33
α-helix	126-129	4
β-strand	137-139	3	33
α-helix	144-146	3
α-helix	147-157	11
β-strand	163-168	6	34
α-helix	171-184	14
β-strand	193-197	5	34
α-helix	205-208	4
α-helix	209-211	3
β-strand	216	1	35
β-strand	218-222	5	34
α-helix	225-237	13
β-strand	246-248	3	34
α-helix	252-254	3
α-helix	257-260	4
α-helix	262-263	2
β-strand	267	1	34
β-strand	270-271	2	36
α-helix	277-296	20
α-helix	303-305	3
α-helix	317-327	11
β-strand	340	1	37
β-strand	346	1	37
β-strand	351-353	3	36
β-strand	356-357	2	38
β-strand	360-361	2	38
β-strand	365-367	3	36
β-strand	372-374	3	36
α-helix	382-384	3
α-helix	388-389	2
β-strand	392	1	35
β-strand	397-402	6	39
β-strand	405	1	40
β-strand	409	1	40
β-strand	410-413	4	41
α-helix	420-422	3
β-strand	424	1	42
α-helix	429	1
β-strand	430	1	42
α-helix	431-432	2
β-strand	434-436	3	41
β-strand	439	1	43
α-helix	448	1
β-strand	450	1	43
β-strand	453-456	4	41
α-helix	458-470	13
β-strand	473-478	6	39
β-strand	487-489	3	44
β-strand	496-498	3	44
α-helix	501-505	5
β-strand	512-513	2	39
β-strand	518	1	45
α-helix	521-524	4
β-strand	527-529	3	39
β-strand	534	1	45
β-strand	538-543	6	46
β-strand	558	1	47
α-helix	560-582	23
α-helix	603-615	13
α-helix	627-656	30
α-helix	670-673	4
β-strand	681-682	2	46
β-strand	684	1	48
α-helix	690-693	4
α-helix	700-707	8
β-strand	711	1	48
α-helix	714-722	9
β-strand	728-732	5	46
α-helix	733-742	10
β-strand	746-753	8	46
β-strand	758	1	45
β-strand	761-763	3	39
α-helix	769-781	13
α-helix	784-788	5
α-helix	789-793	5
β-strand	808	1	31
α-helix	815-840	26

Chain D: 38 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-41	7	49
α-helix	47-56	10
β-strand	66-72	7	49
α-helix	78-91	14
β-strand	96-100	5	49
α-helix	107-119	13
β-strand	123-127	5	49
α-helix	133-134	2
β-strand	143-145	3	49
α-helix	150-163	14
β-strand	168-169	2	50
β-strand	171-173	3	51
α-helix	179-190	12
β-strand	198-199	2	50
β-strand	204	1	51
α-helix	213-220	8
β-strand	227-231	5	51
α-helix	234-247	14
β-strand	255-258	4	51
α-helix	260-263	4
β-strand	278-282	5	51
α-helix	289-310	22
α-helix	325-327	3
α-helix	336-340	5
β-strand	343-344	2	52
β-strand	347-348	2	52
β-strand	351	1	53
β-strand	357	1	53
β-strand	362-367	6	51
β-strand	373-379	7	51
β-strand	385-386	2	51
β-strand	405-410	6	54
β-strand	418-421	4	54
α-helix	422-423	2
β-strand	434-438	5	54
β-strand	453-458	6	54
α-helix	460-472	13
β-strand	475-480	6	54
β-strand	488-490	3	55
β-strand	493-495	3	55
α-helix	497-502	6
β-strand	508	1	54
α-helix	513	1
β-strand	514	1	56
α-helix	515	1
α-helix	517-520	4
β-strand	524	1	57
β-strand	531-534	4	58
β-strand	535-539	5	59
α-helix	540-541	2
α-helix	545-546	2
α-helix	556-560	5
α-helix	561-566	6
α-helix	567-579	13
α-helix	598-600	3
α-helix	602-611	10
α-helix	626-655	30
α-helix	669-672	4
β-strand	683-684	2	59
α-helix	690-697	8
α-helix	700-705	6
α-helix	706-709	4
α-helix	714-723	10
β-strand	728-731	4	59
α-helix	733-742	10
β-strand	748-750	3	59
α-helix	751-753	3
β-strand	757-761	5	58
β-strand	762	1	56
β-strand	766	1	57
α-helix	767	1
α-helix	772-786	15
α-helix	788-792	5
α-helix	793-797	5
β-strand	813	1	47
α-helix	819-843	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	830	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	861	Homo sapiens	Q13224 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9OOQ_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
ARAASDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALS
VCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSF
LRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQF
DPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGN
ALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKT
GPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDR
KIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICT
GPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKE
WNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQP
FQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNS
GIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSD
KFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLE
FEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQE
CDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDANGAQ

Sequence of entity 2 (B, D), FASTA

>9OOQ_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
WSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRGRSQKSPPSIGIAVILVGTSDEVAIK
DAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQI
LDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSI
VTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLY
CTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPA
RVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSF
SEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTL
EEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKS
VKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIE
TGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRSLAD
GREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLA
AFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQ
RGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSG
WKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMAL
SLITFISEHLFYWQFRHSFMG

Ligands and cofactors

ID	Name	Formula	Copies
A1CE1	24S-hydroxycholesterol	C27 H46 O2	2
GLU	Glutamic acid	C5 H9 N O4	2
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	8
GLY	Glycine	C2 H5 N O2	2

Primary citation

Mechanism of conductance control and neurosteroid binding in NMDA receptors. Kang, H., Steigerwald, R., Ullman, E.Z. et al. Nature (2025) 648:220-228. DOI 10.1038/s41586-025-09695-4 · 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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