9IYQ: Glutamate receptor ionotropic, NMDA 1

Structure of the human GluN1-N2B NMDA receptors in the Mg2+ free state. Determined by electron microscopy at 3.18 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Homo sapiens
Chains: 4
Atoms: 23,446
Mol. weight: 381.63 kDa
Ligands: GLY, NAG, 7RC
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9IYQ contains 134 α-helices and 171 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: 33 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	1
α-helix	36-50	15
β-strand	62-65	4	1
α-helix	71-85	15
β-strand	90-92	3	1
α-helix	105-114	10
β-strand	118-120	3	1
β-strand	137-139	3	1
α-helix	147-157	11
β-strand	163-167	5	2
β-strand	168	1	3
α-helix	171-185	15
β-strand	193	1	2
β-strand	197	1	3
α-helix	205-210	6
β-strand	216	1	4
β-strand	218-222	5	2
α-helix	225-232	8
β-strand	247-248	2	2
α-helix	252-254	3
α-helix	258-261	4
α-helix	262-263	2
β-strand	267-271	5	2
α-helix	279-297	19
α-helix	318-325	8
β-strand	340	1	5
β-strand	346	1	5
β-strand	351-357	7	2
β-strand	360-367	8	2
β-strand	372-374	3	2
α-helix	388-389	2
β-strand	392	1	4
β-strand	397	1	6
β-strand	400-402	3	7
β-strand	405	1	8
β-strand	409	1	8
β-strand	410-411	2	9
α-helix	420-422	3
β-strand	424	1	10
β-strand	430	1	10
α-helix	431-432	2
β-strand	433-434	2	9
β-strand	437	1	7
β-strand	452	1	7
β-strand	455-456	2	9
α-helix	458-469	12
β-strand	473	1	6
β-strand	476-478	3	7
β-strand	487-488	2	11
β-strand	497-498	2	11
α-helix	500-507	8
β-strand	512-513	2	7
β-strand	518	1	12
α-helix	521-524	4
β-strand	527-529	3	7
β-strand	534-543	10	12
α-helix	544-546	3
β-strand	558	1	13
α-helix	560-581	22
α-helix	604-615	12
α-helix	627-656	30
α-helix	660-662	3
α-helix	670-673	4
β-strand	681-682	2	12
β-strand	684	1	14
α-helix	688-695	8
α-helix	700-706	7
β-strand	711	1	14
α-helix	714-722	9
β-strand	728-732	5	12
α-helix	733-740	8
β-strand	746-758	13	12
β-strand	761-763	3	7
α-helix	769-782	14
α-helix	784-792	9
α-helix	802-804	3
β-strand	808	1	15
α-helix	810-812	3
α-helix	814-836	23

Chain B: 33 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	16
α-helix	47-53	7
β-strand	67-68	2	16
β-strand	71-73	3	16
α-helix	78-88	11
β-strand	96-101	6	16
α-helix	107-119	13
β-strand	123-127	5	16
α-helix	129-131	3
α-helix	137-138	2
β-strand	143-145	3	16
α-helix	150-163	14
β-strand	169	1	17
β-strand	171-173	3	18
α-helix	179-191	13
β-strand	202-203	2	18
α-helix	210-212	3
α-helix	213-220	8
β-strand	227	1	17
β-strand	230-231	2	18
α-helix	234-247	14
β-strand	255	1	17
β-strand	257-258	2	19
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	19
α-helix	289-309	21
α-helix	317-319	3
α-helix	324-330	7
α-helix	332-339	8
β-strand	351	1	20
β-strand	356	1	16
β-strand	357	1	20
β-strand	362-367	6	19
β-strand	373-379	7	19
β-strand	384	1	19
β-strand	405-410	6	21
β-strand	418-419	2	22
β-strand	437-438	2	21
α-helix	439	1
β-strand	453-454	2	21
β-strand	457-458	2	22
α-helix	460-472	13
β-strand	475-480	6	21
β-strand	490	1	23
β-strand	493	1	23
α-helix	496-502	7
β-strand	508-514	7	21
β-strand	524-525	2	21
β-strand	530-539	10	21
α-helix	547-551	5
β-strand	554	1	24
α-helix	556-578	23
α-helix	602-613	12
α-helix	626-653	28
α-helix	669-672	4
α-helix	674-676	3
β-strand	684-685	2	21
α-helix	690-698	9
α-helix	700-705	6
α-helix	706-708	3
α-helix	715-723	9
β-strand	729-732	4	21
α-helix	733-741	9
β-strand	748-750	3	21
β-strand	757-766	10	21
α-helix	772-786	15
α-helix	788-796	9
β-strand	813	1	13
α-helix	819-837	19

Chain C: 37 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	25
α-helix	36-51	16
β-strand	62-66	5	25
α-helix	71-84	14
β-strand	87-92	6	25
α-helix	105-114	10
β-strand	118-120	3	25
α-helix	127-129	3
β-strand	137-139	3	25
α-helix	144-146	3
α-helix	147-157	11
β-strand	163-167	5	26
β-strand	168	1	27
α-helix	171-185	15
β-strand	193-194	2	26
β-strand	197	1	27
α-helix	205-212	8
β-strand	216	1	28
β-strand	218-222	5	26
α-helix	225-232	8
α-helix	236-238	3
β-strand	247-248	2	26
α-helix	256-261	6
α-helix	262-263	2
β-strand	267-271	5	26
α-helix	278-297	20
α-helix	302-305	4
α-helix	318-325	8
β-strand	330-333	4	29
β-strand	336-338	3	29
β-strand	340	1	30
β-strand	346	1	30
β-strand	351-357	7	26
β-strand	360-367	8	26
β-strand	372-374	3	26
β-strand	392	1	28
β-strand	397-402	6	31
β-strand	410-412	3	31
α-helix	413-415	3
α-helix	420-422	3
β-strand	424	1	32
α-helix	429	1
β-strand	430	1	32
α-helix	431-432	2
β-strand	434-438	5	31
β-strand	451-456	6	31
α-helix	458-469	12
β-strand	473-478	6	31
β-strand	488	1	33
β-strand	497	1	33
α-helix	500-507	8
β-strand	512-513	2	31
β-strand	518	1	34
α-helix	521-524	4
β-strand	527-529	3	31
β-strand	534-543	10	34
α-helix	544-546	3
β-strand	558	1	35
α-helix	560-580	21
α-helix	604-615	12
α-helix	627-656	30
α-helix	660-663	4
α-helix	670-673	4
β-strand	681-682	2	34
β-strand	684	1	36
α-helix	688-695	8
α-helix	700-707	8
β-strand	711	1	36
α-helix	714-722	9
β-strand	728-732	5	34
α-helix	733-740	8
β-strand	746-758	13	34
β-strand	761-763	3	31
α-helix	769-782	14
α-helix	784-792	9
α-helix	803-806	4
β-strand	808	1	24
α-helix	811-813	3
α-helix	815-836	22

Chain D: 31 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	37
α-helix	49-55	7
α-helix	58-61	4
β-strand	67-68	2	37
β-strand	71-73	3	37
α-helix	78-91	14
β-strand	96-100	5	37
α-helix	107-119	13
β-strand	123-125	3	37
α-helix	129-131	3
α-helix	137-138	2
β-strand	143-145	3	37
α-helix	150-163	14
β-strand	169	1	38
β-strand	171-173	3	39
α-helix	179-191	13
β-strand	202-203	2	39
α-helix	213-219	7
β-strand	227	1	38
β-strand	230-231	2	39
α-helix	234-247	14
β-strand	255	1	38
β-strand	257-258	2	40
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	40
α-helix	289-309	21
α-helix	324-330	7
α-helix	332-338	7
β-strand	351	1	41
β-strand	356	1	37
β-strand	357	1	41
β-strand	362-367	6	40
β-strand	373-379	7	40
β-strand	405-410	6	42
β-strand	413	1	43
β-strand	417	1	43
β-strand	418-419	2	44
β-strand	437-438	2	42
β-strand	439	1	45
β-strand	452	1	45
β-strand	457-458	2	44
α-helix	460-472	13
β-strand	475-480	6	42
β-strand	490	1	46
β-strand	493	1	46
α-helix	496-502	7
β-strand	508-510	3	42
β-strand	514	1	47
β-strand	524	1	48
β-strand	530-539	10	47
β-strand	541	1	49
α-helix	549-551	3
β-strand	554	1	15
α-helix	556-578	23
α-helix	602-613	12
α-helix	626-653	28
β-strand	656	1	50
β-strand	659	1	49
α-helix	669-672	4
β-strand	683-684	2	47
α-helix	690-698	9
α-helix	700-706	7
α-helix	707-709	3
α-helix	715-723	9
β-strand	728-732	5	47
α-helix	733-741	9
β-strand	748-750	3	47
β-strand	757-762	6	47
β-strand	765	1	42
β-strand	766	1	48
α-helix	772-786	15
α-helix	788-796	9
α-helix	800-802	3
β-strand	809	1	50
β-strand	813	1	35
α-helix	819-837	19

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 2B	B, D	protein	842	Homo sapiens	Q13224 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9IYQ_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

>9IYQ_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFH
HLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTL
TPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQ
DFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYI
FEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAII
TTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHP
KLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTLEEAPFVIVE
SVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYL
VTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSR
SNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSF
TIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYV
DQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLS
LKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAI
LQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEH
LF

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
7RC	(2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid	C8 H17 N2 O5 P	2

Primary citation

Structural insights into the diverse actions of magnesium on NMDA receptors. Huang, X., Sun, X., Wang, Q. et al. Neuron (2025) 113:1006. DOI 10.1016/j.neuron.2025.01.021 · 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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