9OOS: Glutamate receptor ionotropic, NMDA 1

Non-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR. Determined by electron microscopy at 3.03 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,629
Mol. weight: 384.16 kDa
Ligands: GLY, POV, A8W, GLU
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9OOS contains 146 α-helices and 165 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: 39 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	32	1	2
α-helix	36-49	14
β-strand	59-61	3	1
β-strand	65	1	2
α-helix	66-68	3
α-helix	72-85	14
β-strand	90-92	3	2
α-helix	105-113	9
β-strand	118-120	3	2
α-helix	126-129	4
β-strand	138-139	2	2
α-helix	144-146	3
α-helix	147-158	12
β-strand	163-168	6	3
α-helix	171-184	14
β-strand	193	1	3
β-strand	196-197	2	3
α-helix	205-210	6
β-strand	216	1	4
β-strand	218-222	5	3
α-helix	225-237	13
β-strand	246-249	4	3
α-helix	252-254	3
α-helix	258-261	4
α-helix	262-263	2
β-strand	267-271	5	3
α-helix	277-292	16
α-helix	301-305	5
α-helix	317-327	11
β-strand	330	1	5
β-strand	338	1	5
β-strand	339-340	2	6
β-strand	346-347	2	6
β-strand	351-357	7	3
β-strand	360-367	8	3
β-strand	372-374	3	3
α-helix	382-384	3
α-helix	388-389	2
β-strand	392	1	4
β-strand	397-402	6	7
β-strand	405	1	8
β-strand	409	1	8
β-strand	410-412	3	9
α-helix	413-415	3
α-helix	420-422	3
β-strand	424	1	10
α-helix	429	1
β-strand	430	1	10
α-helix	431-432	2
β-strand	434-435	2	9
α-helix	440	1
β-strand	454-456	3	9
α-helix	458-470	13
β-strand	473-478	6	7
β-strand	488-490	3	11
β-strand	495-497	3	11
α-helix	500-506	7
β-strand	512-518	7	7
α-helix	521-524	4
β-strand	528-529	2	7
β-strand	534	1	7
β-strand	538-543	6	12
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	12
β-strand	684	1	13
α-helix	690-693	4
α-helix	697-699	3
α-helix	700-707	8
β-strand	711	1	13
α-helix	714-722	9
β-strand	728-732	5	12
α-helix	733-742	10
β-strand	746-753	8	12
β-strand	758-762	5	7
α-helix	769-781	13
α-helix	784-789	6
α-helix	790-794	5
β-strand	808	1	14
α-helix	810-839	30

Chain B: 35 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-42	8	15
α-helix	47-56	10
β-strand	66-73	8	15
α-helix	78-92	15
β-strand	96-99	4	15
α-helix	107-119	13
β-strand	123-125	3	15
α-helix	128-131	4
β-strand	143-145	3	15
α-helix	150-163	14
β-strand	168-169	2	16
β-strand	171-173	3	17
α-helix	179-190	12
β-strand	198-199	2	16
β-strand	204	1	17
α-helix	213-221	9
β-strand	227-231	5	17
α-helix	234-247	14
β-strand	255-258	4	17
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	17
α-helix	289-310	22
α-helix	324-329	6
α-helix	333-339	7
β-strand	344	1	18
β-strand	347	1	18
α-helix	350	1
β-strand	351	1	19
α-helix	352	1
β-strand	357	1	19
β-strand	362-367	6	17
β-strand	373-380	8	17
β-strand	383-386	4	17
β-strand	405-410	6	20
β-strand	413	1	21
β-strand	417	1	21
β-strand	418-420	3	20
α-helix	421-423	3
β-strand	434-438	5	20
β-strand	453-458	6	20
α-helix	460-472	13
β-strand	475-480	6	20
β-strand	488-490	3	22
β-strand	493-495	3	22
α-helix	497-502	6
β-strand	508	1	20
α-helix	513	1
β-strand	514	1	23
α-helix	515	1
α-helix	517-520	4
β-strand	524-525	2	20
β-strand	530-539	10	23
α-helix	549-551	3
α-helix	556-575	20
α-helix	602-613	12
α-helix	626-655	30
α-helix	669-672	4
β-strand	683-684	2	23
α-helix	690-698	9
α-helix	700-707	8
α-helix	714-723	10
β-strand	728-732	5	23
α-helix	733-739	7
α-helix	744-746	3
β-strand	748-750	3	23
α-helix	751-754	4
β-strand	757-762	6	23
β-strand	765-766	2	20
α-helix	773-786	14
α-helix	788-796	9
α-helix	815-844	30

Chain C: 37 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	24
β-strand	32	1	25
α-helix	36-51	16
β-strand	59-61	3	24
β-strand	65	1	25
α-helix	71-78	8
α-helix	80-85	6
β-strand	87	1	24
β-strand	90-92	3	26
α-helix	105-113	9
β-strand	118-120	3	26
α-helix	127-129	3
β-strand	138-139	2	26
α-helix	144-146	3
α-helix	147-158	12
β-strand	163-167	5	27
β-strand	168	1	28
α-helix	171-180	10
α-helix	185-187	3
β-strand	193	1	27
β-strand	197	1	28
α-helix	205-212	8
β-strand	216	1	29
β-strand	218-222	5	27
α-helix	225-236	12
β-strand	246-249	4	27
α-helix	252-254	3
α-helix	258-261	4
β-strand	267-271	5	27
α-helix	277-296	20
α-helix	303-305	3
α-helix	317-322	6
β-strand	330	1	30
β-strand	338	1	30
β-strand	340	1	31
β-strand	346	1	31
β-strand	351-356	6	27
β-strand	361-367	7	27
β-strand	372-374	3	27
α-helix	382-384	3
α-helix	388-389	2
β-strand	392	1	29
β-strand	397-402	6	32
β-strand	410-413	4	33
α-helix	414-415	2
β-strand	424	1	34
α-helix	429	1
β-strand	430	1	34
α-helix	431-432	2
β-strand	434-436	3	33
β-strand	453-456	4	33
α-helix	458-470	13
β-strand	473-478	6	32
β-strand	487-488	2	35
β-strand	497-498	2	35
α-helix	500-506	7
β-strand	512-518	7	32
α-helix	519	1
α-helix	521-524	4
β-strand	528-529	2	32
β-strand	534	1	32
β-strand	538-543	6	36
β-strand	558	1	37
α-helix	562-582	21
α-helix	603-615	13
α-helix	627-656	30
α-helix	670-673	4
β-strand	681-682	2	36
β-strand	684	1	38
α-helix	690-693	4
α-helix	700-707	8
β-strand	711	1	38
α-helix	714-722	9
β-strand	728-732	5	36
α-helix	733-742	10
β-strand	746-753	8	36
β-strand	758-762	5	32
α-helix	769-781	13
α-helix	784-792	9
α-helix	810-820	11
α-helix	822-840	19

Chain D: 35 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	35-42	8	39
α-helix	47-56	10
β-strand	66-73	8	39
α-helix	78-92	15
β-strand	96-99	4	39
α-helix	108-119	12
β-strand	123-125	3	39
α-helix	128-131	4
β-strand	144-145	2	39
β-strand	147	1	40
α-helix	150-163	14
β-strand	168-169	2	41
β-strand	171-173	3	42
α-helix	179-190	12
β-strand	198-199	2	41
β-strand	204	1	42
α-helix	213-220	8
β-strand	227-231	5	42
α-helix	234-247	14
β-strand	255-258	4	42
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	42
α-helix	289-307	19
α-helix	324-328	5
α-helix	335-339	5
β-strand	343-344	2	43
β-strand	347-348	2	43
β-strand	356	1	40
β-strand	362-367	6	42
β-strand	373-380	8	42
β-strand	383-386	4	42
β-strand	405-410	6	44
β-strand	413	1	45
β-strand	417	1	45
β-strand	418-420	3	44
α-helix	421-423	3
β-strand	434-439	6	44
β-strand	452-458	7	44
α-helix	460-472	13
β-strand	475-480	6	44
β-strand	488-490	3	46
β-strand	493-495	3	46
α-helix	497-502	6
β-strand	508	1	44
β-strand	513-514	2	47
α-helix	515	1
α-helix	517-520	4
β-strand	524-525	2	48
β-strand	530-534	5	47
β-strand	535-539	5	49
α-helix	549-551	3
β-strand	554	1	14
α-helix	556-575	20
α-helix	602-613	12
α-helix	627-655	29
α-helix	669-672	4
β-strand	683-684	2	49
α-helix	690-698	9
α-helix	700-705	6
α-helix	706-709	4
α-helix	714-723	10
β-strand	728-731	4	49
α-helix	733-742	10
α-helix	744-746	3
β-strand	748-750	3	49
α-helix	751-754	4
β-strand	757-763	7	47
β-strand	765-766	2	48
α-helix	767	1
α-helix	772-786	15
α-helix	788-792	5
α-helix	793-797	5
β-strand	813	1	37
α-helix	819-844	26

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

>9OOS_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

>9OOS_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
GLY	Glycine	C2 H5 N O2	2
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	4
A8W	Pregnenolone sulfate	C21 H32 O5 S	4
GLU	Glutamic acid	C5 H9 N O4	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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