9OOT: Glutamate receptor ionotropic, NMDA 1

Pre-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR. Determined by electron microscopy at 3.13 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.13 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,825
Mol. weight: 384.16 kDa
Ligands: A8W, GLU, POV, GLY
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9OOT contains 137 α-helices and 174 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: 37 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	32	1	2
α-helix	36-51	16
β-strand	59-61	3	1
β-strand	65	1	2
α-helix	66-68	3
α-helix	71-85	15
β-strand	90-92	3	3
α-helix	105-110	6
β-strand	118-120	3	3
α-helix	126-129	4
β-strand	138-139	2	3
α-helix	144-146	3
α-helix	147-158	12
β-strand	163-167	5	4
β-strand	168	1	5
α-helix	171-186	16
β-strand	193	1	4
β-strand	197	1	5
α-helix	205-213	9
β-strand	216	1	6
β-strand	218-222	5	4
α-helix	225-237	13
β-strand	246-249	4	4
α-helix	252-254	3
α-helix	257-260	4
α-helix	262-263	2
β-strand	267-271	5	4
α-helix	277-296	20
α-helix	303-305	3
α-helix	317-326	10
β-strand	340	1	7
β-strand	346	1	7
β-strand	351-357	7	4
β-strand	360-367	8	4
β-strand	372-373	2	4
α-helix	378-379	2
α-helix	382-384	3
α-helix	388-389	2
β-strand	392	1	6
β-strand	397-402	6	8
β-strand	405	1	9
β-strand	409	1	9
β-strand	410-413	4	10
α-helix	414-415	2
β-strand	424	1	11
α-helix	429	1
β-strand	430	1	11
α-helix	431-432	2
β-strand	434-436	3	10
β-strand	453-456	4	10
α-helix	458-470	13
β-strand	473-478	6	8
β-strand	487-488	2	12
β-strand	497-498	2	12
α-helix	500-507	8
β-strand	512-513	2	8
β-strand	518	1	13
α-helix	521-524	4
β-strand	528	1	14
β-strand	534	1	13
β-strand	538-543	6	15
β-strand	558	1	16
α-helix	560-581	22
α-helix	603-615	13
α-helix	627-656	30
α-helix	666-668	3
β-strand	681-682	2	17
β-strand	684	1	18
α-helix	688-694	7
α-helix	701-707	7
β-strand	711	1	18
α-helix	714-722	9
β-strand	728-729	2	17
β-strand	730-732	3	15
α-helix	733-742	10
β-strand	746-749	4	15
β-strand	758	1	13
β-strand	761	1	8
β-strand	762	1	14
α-helix	769-782	14
α-helix	784-792	9
α-helix	805-807	3
β-strand	808	1	19
α-helix	810-840	31

Chain B: 34 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-41	7	20
α-helix	47-56	10
β-strand	66-72	7	20
α-helix	78-92	15
β-strand	96-99	4	20
α-helix	107-119	13
β-strand	123-125	3	20
α-helix	128-131	4
β-strand	143-145	3	20
α-helix	150-163	14
β-strand	171-173	3	21
α-helix	179-191	13
β-strand	204	1	21
α-helix	213-219	7
α-helix	220-222	3
β-strand	229-231	3	21
α-helix	234-247	14
β-strand	257-258	2	21
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	21
α-helix	289-310	22
α-helix	325-327	3
α-helix	333-340	8
β-strand	344	1	22
β-strand	347	1	22
β-strand	351	1	23
β-strand	357	1	23
β-strand	362-367	6	21
β-strand	373-380	8	21
β-strand	383-384	2	21
β-strand	405-410	6	24
β-strand	418-420	3	24
α-helix	421-423	3
β-strand	434-437	4	24
β-strand	455-458	4	24
α-helix	460-472	13
β-strand	475-480	6	24
β-strand	490	1	25
β-strand	493	1	25
α-helix	496-502	7
β-strand	508	1	24
α-helix	513	1
β-strand	514	1	26
α-helix	515	1
α-helix	517-520	4
β-strand	524	1	24
β-strand	531-532	2	27
β-strand	535-536	2	28
β-strand	537-539	3	29
α-helix	549-551	3
α-helix	556-572	17
α-helix	573-577	5
α-helix	602-613	12
α-helix	626-655	30
α-helix	669-672	4
β-strand	683-684	2	30
α-helix	690-698	9
α-helix	700-705	6
α-helix	714-722	9
β-strand	728-729	2	30
β-strand	730-731	2	28
α-helix	733-742	10
β-strand	748-750	3	29
β-strand	760-761	2	27
β-strand	762	1	26
β-strand	766	1	24
α-helix	767	1
α-helix	772-785	14
α-helix	788-796	9
β-strand	813	1	16
α-helix	815-844	30

Chain C: 32 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	31
β-strand	32	1	32
α-helix	36-51	16
β-strand	59-61	3	31
β-strand	65	1	32
α-helix	66-68	3
α-helix	71-83	13
β-strand	90-92	3	32
α-helix	105-112	8
β-strand	118-120	3	32
α-helix	126-129	4
β-strand	138-139	2	32
α-helix	144-146	3
α-helix	147-158	12
β-strand	163-165	3	33
β-strand	168	1	34
α-helix	171-186	16
β-strand	193	1	33
β-strand	197	1	34
α-helix	205-212	8
β-strand	216	1	35
β-strand	218-221	4	33
α-helix	225-237	13
β-strand	246-249	4	33
α-helix	252-254	3
β-strand	267	1	33
β-strand	270-271	2	36
α-helix	277-296	20
α-helix	303-305	3
α-helix	317-327	11
β-strand	339-340	2	37
β-strand	346-347	2	37
β-strand	351-352	2	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	398-402	5	39
β-strand	405	1	40
β-strand	409	1	40
β-strand	410-413	4	41
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	453-456	4	41
α-helix	458-470	13
β-strand	474-478	5	39
β-strand	487-488	2	43
β-strand	497-498	2	43
α-helix	501-506	6
β-strand	512-513	2	39
β-strand	518	1	44
α-helix	521-526	6
β-strand	528-529	2	39
β-strand	534	1	44
β-strand	538-543	6	45
β-strand	558	1	46
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	45
β-strand	684	1	47
α-helix	688-695	8
α-helix	700-707	8
β-strand	711	1	47
α-helix	714-722	9
β-strand	728-732	5	45
α-helix	733-742	10
β-strand	746-748	3	45
β-strand	753	1	45
β-strand	758	1	44
β-strand	761-762	2	39
α-helix	769-781	13
α-helix	784-792	9
α-helix	810-840	31

Chain D: 34 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-41	7	48
α-helix	47-56	10
β-strand	66-72	7	48
α-helix	78-92	15
β-strand	96-99	4	48
α-helix	107-117	11
β-strand	123-125	3	48
α-helix	128-131	4
β-strand	143-145	3	48
α-helix	150-163	14
β-strand	168-169	2	49
β-strand	171-173	3	50
α-helix	179-191	13
β-strand	198-199	2	49
β-strand	204	1	50
α-helix	213-220	8
β-strand	229-231	3	50
α-helix	234-247	14
β-strand	257-259	3	50
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	50
α-helix	289-306	18
α-helix	307-311	5
α-helix	326-329	4
α-helix	333-340	8
β-strand	343-344	2	51
β-strand	347-348	2	51
β-strand	351	1	52
β-strand	357	1	52
β-strand	362-367	6	50
β-strand	373-375	3	50
β-strand	379-380	2	50
β-strand	383-384	2	50
β-strand	405-410	6	53
β-strand	418-420	3	53
α-helix	421-423	3
β-strand	434-438	5	53
β-strand	453-458	6	53
α-helix	460-472	13
β-strand	475-480	6	53
β-strand	488-490	3	54
β-strand	493-495	3	54
α-helix	497-502	6
β-strand	508	1	53
α-helix	513-515	3
α-helix	519-521	3
β-strand	524	1	53
β-strand	531-534	4	55
β-strand	535-536	2	56
β-strand	538-539	2	57
α-helix	540-541	2
β-strand	554	1	19
α-helix	556-571	16
α-helix	572-576	5
α-helix	602-613	12
α-helix	626-655	30
α-helix	669-672	4
α-helix	680-682	3
β-strand	683-685	3	56
α-helix	690-698	9
α-helix	700-705	6
α-helix	714-723	10
β-strand	728-731	4	56
α-helix	733-742	10
α-helix	744-746	3
β-strand	748-749	2	57
β-strand	757-761	5	55
β-strand	766	1	53
α-helix	772-786	15
α-helix	788-796	9
β-strand	813	1	46
α-helix	815-844	30

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

>9OOT_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

>9OOT_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
A8W	Pregnenolone sulfate	C21 H32 O5 S	4
GLU	Glutamic acid	C5 H9 N O4	2
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	4
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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