9OOR: Open state Gly/Glu/24S-HC bound hGluN1a-2B NMDAR

Open state Gly/Glu/24S-HC bound hGluN1a-2B NMDAR. Determined by electron microscopy at 3.15 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 24,828
Mol. weight: 386.42 kDa
Ligands: GLY, POV, A1CE1, GLU
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9OOR contains 160 α-helices and 182 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, 51 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	87	1	1
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	147-157	11
β-strand	163-165	3	3
β-strand	168	1	4
α-helix	171-187	17
β-strand	193	1	3
β-strand	197	1	4
α-helix	205-212	8
β-strand	216	1	5
β-strand	218-221	4	3
α-helix	225-237	13
β-strand	246-249	4	3
α-helix	251-254	4
α-helix	257-261	5
α-helix	262-263	2
β-strand	267-271	5	3
α-helix	277-296	20
α-helix	302-304	3
α-helix	317-327	11
β-strand	330	1	6
β-strand	338	1	6
β-strand	339-340	2	7
β-strand	346-347	2	7
β-strand	351-357	7	3
β-strand	360-367	8	3
β-strand	372-374	3	3
α-helix	380-381	2
α-helix	382-384	3
α-helix	388-389	2
β-strand	392	1	5
β-strand	397-402	6	8
β-strand	405	1	9
β-strand	409	1	9
β-strand	410-413	4	10
α-helix	420-422	3
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	439	1	12
β-strand	450	1	12
β-strand	453-456	4	10
α-helix	458-470	13
β-strand	473-478	6	8
β-strand	486-490	5	13
β-strand	495-499	5	13
α-helix	501-506	6
β-strand	512-513	2	8
β-strand	518	1	14
α-helix	521-526	6
β-strand	528	1	15
β-strand	538-543	6	16
α-helix	553-555	3
α-helix	560-582	23
α-helix	603-615	13
α-helix	627-648	22
α-helix	651-656	6
α-helix	670-673	4
β-strand	681-682	2	16
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	16
α-helix	733-742	10
β-strand	746-748	3	16
β-strand	753	1	16
β-strand	758	1	14
β-strand	761	1	8
β-strand	762	1	15
α-helix	769-781	13
α-helix	784-792	9
α-helix	805-807	3
β-strand	808	1	18
α-helix	814-840	27

Chain B: 42 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	35-42	8	19
α-helix	47-56	10
β-strand	66-68	3	19
β-strand	71-73	3	19
α-helix	78-92	15
β-strand	96-100	5	19
α-helix	107-119	13
β-strand	123-125	3	19
α-helix	128-131	4
β-strand	143-145	3	19
α-helix	150-163	14
β-strand	168	1	20
β-strand	172-173	2	21
α-helix	179-191	13
β-strand	198	1	20
β-strand	204	1	21
α-helix	213-220	8
β-strand	227-229	3	22
β-strand	230-231	2	21
α-helix	234-247	14
β-strand	255-259	5	22
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	22
α-helix	289-310	22
α-helix	326-328	3
α-helix	333-335	3
α-helix	336-340	5
β-strand	343-344	2	23
β-strand	347-348	2	23
β-strand	351	1	24
β-strand	357	1	24
β-strand	362-367	6	22
β-strand	373-380	8	22
β-strand	383-384	2	22
β-strand	405-410	6	25
β-strand	413	1	26
α-helix	414-416	3
β-strand	417	1	26
β-strand	418-420	3	25
α-helix	421-423	3
β-strand	434-438	5	25
β-strand	453-458	6	25
α-helix	460-472	13
β-strand	475-480	6	25
β-strand	488-490	3	27
β-strand	493-495	3	27
α-helix	499-502	4
β-strand	508	1	25
α-helix	513	1
β-strand	514	1	28
α-helix	515	1
α-helix	517-520	4
β-strand	524	1	29
β-strand	531-534	4	30
β-strand	535-539	5	31
α-helix	540-543	4
β-strand	544	1	32
α-helix	545-546	2
β-strand	554	1	33
α-helix	556-560	5
α-helix	561-566	6
α-helix	567-580	14
α-helix	598-600	3
α-helix	602-613	12
α-helix	626-647	22
α-helix	650-654	5
β-strand	658	1	32
α-helix	669-672	4
β-strand	683-684	2	31
α-helix	690-698	9
α-helix	700-706	7
α-helix	707-709	3
α-helix	714-723	10
β-strand	728-731	4	31
α-helix	733-741	9
β-strand	748-750	3	31
α-helix	751-754	4
β-strand	757-761	5	30
β-strand	762	1	28
β-strand	766	1	29
α-helix	767	1
α-helix	772-786	15
α-helix	788-796	9
α-helix	814-817	4
α-helix	819-844	26

Chain C: 39 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	27-32	6	34
α-helix	36-51	16
β-strand	60-65	6	34
α-helix	72-85	14
β-strand	87-92	6	34
α-helix	105-113	9
β-strand	118-120	3	34
α-helix	126-129	4
β-strand	138-139	2	34
α-helix	144-146	3
α-helix	147-157	11
β-strand	163-165	3	35
β-strand	168	1	36
α-helix	171-184	14
α-helix	185-187	3
β-strand	193-194	2	35
β-strand	197	1	36
α-helix	205-212	8
β-strand	216	1	37
β-strand	218-221	4	35
α-helix	225-234	10
β-strand	246-249	4	35
α-helix	252-254	3
α-helix	257-261	5
α-helix	262-263	2
β-strand	267-271	5	35
α-helix	278-297	20
α-helix	301-304	4
α-helix	314-315	2
α-helix	318-326	9
β-strand	330	1	38
β-strand	338	1	38
β-strand	340	1	39
β-strand	346	1	39
β-strand	351-357	7	35
β-strand	360-367	8	35
β-strand	372	1	35
α-helix	382-384	3
β-strand	392	1	37
β-strand	397-402	6	40
β-strand	405	1	41
β-strand	409	1	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	434-435	2	42
β-strand	439	1	44
β-strand	450	1	44
β-strand	453-456	4	42
α-helix	458-470	13
β-strand	473-478	6	40
β-strand	486-490	5	45
β-strand	495-499	5	45
α-helix	501-506	6
β-strand	512-513	2	40
β-strand	518	1	46
α-helix	521-526	6
β-strand	528	1	47
β-strand	534	1	46
β-strand	538-542	5	48
α-helix	553-555	3
α-helix	560-582	23
α-helix	603-615	13
α-helix	627-648	22
α-helix	651-656	6
α-helix	670-673	4
β-strand	681-682	2	48
β-strand	684	1	49
α-helix	688-695	8
α-helix	701-709	9
β-strand	711	1	49
α-helix	714-722	9
β-strand	728-732	5	48
α-helix	733-742	10
β-strand	747-753	7	48
β-strand	758	1	46
β-strand	761	1	40
β-strand	762	1	47
α-helix	769-781	13
α-helix	784-788	5
α-helix	789-793	5
α-helix	804-807	4
β-strand	808	1	33
α-helix	814-840	27

Chain D: 40 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-41	7	50
α-helix	47-56	10
β-strand	66-72	7	50
α-helix	78-92	15
β-strand	96-100	5	50
α-helix	107-118	12
β-strand	123-125	3	50
α-helix	128-131	4
β-strand	143-145	3	50
α-helix	150-163	14
β-strand	168-174	7	51
α-helix	179-191	13
β-strand	198-205	8	51
α-helix	213-221	9
β-strand	227-231	5	51
α-helix	234-247	14
β-strand	255-258	4	51
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	51
α-helix	289-310	22
α-helix	324-328	5
α-helix	333-335	3
α-helix	336-340	5
β-strand	343-344	2	52
β-strand	347-348	2	52
α-helix	350	1
β-strand	351	1	53
α-helix	352	1
β-strand	357	1	53
β-strand	362-367	6	51
β-strand	373-379	7	51
β-strand	384	1	51
β-strand	406-410	5	54
β-strand	413	1	55
β-strand	417	1	55
β-strand	418-421	4	54
β-strand	434-437	4	54
β-strand	454-458	5	54
α-helix	460-472	13
β-strand	476-480	5	54
β-strand	489-490	2	56
β-strand	493-494	2	56
α-helix	496-502	7
β-strand	508-509	2	54
α-helix	513	1
β-strand	514	1	57
α-helix	515	1
α-helix	517-520	4
β-strand	524-525	2	58
β-strand	531-539	9	59
α-helix	540-541	2
β-strand	544	1	60
α-helix	545-546	2
β-strand	554	1	18
α-helix	556-560	5
α-helix	561-565	5
α-helix	566-580	15
α-helix	603-613	11
α-helix	626-648	23
α-helix	650-655	6
β-strand	658	1	60
α-helix	669-672	4
β-strand	683-684	2	59
α-helix	690-698	9
α-helix	700-705	6
α-helix	714-723	10
β-strand	728-732	5	59
α-helix	733-741	9
β-strand	748-750	3	59
α-helix	751-754	4
β-strand	757-761	5	59
β-strand	762	1	57
β-strand	765-766	2	58
α-helix	767	1
α-helix	772-786	15
α-helix	788-796	9
α-helix	804-807	4
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

>9OOR_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

>9OOR_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	8
A1CE1	24S-hydroxycholesterol	C27 H46 O2	2
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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