9IYP: Glutamate receptor ionotropic, NMDA 1

Structure of the human GluN1-N2B NMDA receptors in the Mg2+ bound state. Determined by electron microscopy at 3.27 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 3.27 Å
Organism: Homo sapiens
Chains: 4
Atoms: 23,443
Mol. weight: 365.97 kDa
Ligands: GLY, NAG, 7RC, MG
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9IYP contains 131 α-helices and 166 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, 41 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	1
α-helix	36-52	17
β-strand	61-66	6	1
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	105-114	10
β-strand	118-120	3	1
β-strand	137-139	3	1
α-helix	144-146	3
α-helix	147-154	8
β-strand	163-167	5	2
β-strand	168	1	3
α-helix	171-186	16
β-strand	193	1	2
β-strand	197	1	3
α-helix	205-212	8
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-248	3	2
α-helix	252-254	3
α-helix	257-261	5
α-helix	262-263	2
β-strand	266-271	6	2
α-helix	277-295	19
α-helix	303-305	3
α-helix	322-327	6
β-strand	330	1	4
β-strand	338	1	4
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	378-379	2
β-strand	397-402	6	6
β-strand	410-412	3	6
α-helix	420-422	3
β-strand	424	1	7
β-strand	430	1	7
β-strand	434-437	4	6
β-strand	452-456	5	6
α-helix	458-469	12
β-strand	473-478	6	6
β-strand	488	1	8
β-strand	497	1	8
α-helix	500-507	8
β-strand	512-513	2	6
β-strand	518	1	9
α-helix	521-524	4
β-strand	527-529	3	6
β-strand	534-543	10	9
β-strand	558	1	10
α-helix	560-583	24
α-helix	604-614	11
α-helix	627-656	30
α-helix	670-673	4
β-strand	681-682	2	9
β-strand	684	1	11
α-helix	688-695	8
α-helix	700-707	8
β-strand	711	1	11
α-helix	714-722	9
β-strand	728-732	5	9
α-helix	733-739	7
β-strand	746-748	3	9
β-strand	753-758	6	9
β-strand	761-763	3	6
α-helix	769-782	14
α-helix	784-792	9
α-helix	803-804	2
β-strand	808	1	12
α-helix	813-839	27

Chain B: 33 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	13
α-helix	47-54	8
β-strand	68-73	6	13
α-helix	78-90	13
β-strand	94-99	6	13
α-helix	106-119	14
β-strand	123-125	3	13
α-helix	128-131	4
α-helix	137-138	2
β-strand	143-145	3	13
α-helix	150-163	14
β-strand	169	1	14
β-strand	171-173	3	15
α-helix	179-191	13
β-strand	202-203	2	15
α-helix	213-220	8
β-strand	227	1	14
β-strand	230-231	2	15
α-helix	234-247	14
β-strand	255	1	14
β-strand	257-258	2	16
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	16
α-helix	289-293	5
α-helix	297-311	15
α-helix	324-327	4
α-helix	334-339	6
α-helix	347-349	3
β-strand	351	1	17
β-strand	357	1	17
β-strand	362-366	5	16
β-strand	374-380	7	16
β-strand	383-385	3	16
β-strand	405-410	6	18
β-strand	418	1	19
β-strand	434-439	6	18
β-strand	452-457	6	18
β-strand	458	1	19
α-helix	460-472	13
β-strand	475-480	6	18
β-strand	490	1	20
β-strand	493	1	20
α-helix	496-502	7
β-strand	508-509	2	18
β-strand	514	1	21
α-helix	517-520	4
β-strand	524	1	22
β-strand	530-539	10	21
α-helix	547-551	5
β-strand	554	1	23
α-helix	556-577	22
α-helix	602-614	13
α-helix	626-653	28
β-strand	656	1	24
α-helix	669-672	4
β-strand	683-685	3	21
α-helix	690-698	9
α-helix	701-706	6
α-helix	714-723	10
β-strand	728-732	5	21
α-helix	733-740	8
β-strand	748-750	3	21
α-helix	753-755	3
β-strand	757-762	6	21
β-strand	765	1	18
β-strand	766	1	22
α-helix	772-786	15
α-helix	788-792	5
α-helix	793-797	5
β-strand	809	1	24
β-strand	813	1	10
α-helix	819-841	23

Chain C: 34 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	28-29	2	25
β-strand	30-33	4	26
α-helix	36-52	17
β-strand	61-62	2	25
β-strand	65-66	2	26
α-helix	71-78	8
α-helix	79-83	5
β-strand	90-93	4	26
α-helix	105-112	8
β-strand	118-121	4	26
α-helix	127-129	3
β-strand	138-139	2	26
α-helix	148-158	11
β-strand	163-168	6	27
α-helix	171-186	16
β-strand	193-197	5	27
α-helix	205-212	8
β-strand	216	1	28
β-strand	218-222	5	27
α-helix	225-237	13
β-strand	246-248	3	27
α-helix	257-261	5
α-helix	263	1
β-strand	267	1	27
β-strand	268-271	4	29
α-helix	277-297	21
α-helix	303-305	3
α-helix	314-315	2
α-helix	319-327	9
β-strand	340	1	30
β-strand	346	1	30
β-strand	350-357	8	29
β-strand	360-368	9	29
β-strand	371-374	4	29
α-helix	382-384	3
β-strand	392	1	28
β-strand	397-402	6	31
β-strand	405	1	32
β-strand	409-412	4	32
β-strand	425	1	33
β-strand	428	1	33
β-strand	434-438	5	32
β-strand	451-457	7	32
α-helix	458-470	13
β-strand	473-478	6	31
β-strand	485-489	5	34
β-strand	496-500	5	34
α-helix	501-507	7
β-strand	512-513	2	31
β-strand	518	1	35
α-helix	521-524	4
β-strand	528-529	2	31
β-strand	534-536	3	35
β-strand	540-542	3	36
α-helix	545-547	3
β-strand	558	1	37
α-helix	560-583	24
α-helix	604-614	11
α-helix	627-656	30
α-helix	660-664	5
α-helix	670-673	4
β-strand	682	1	36
α-helix	688-695	8
α-helix	697-699	3
α-helix	700-707	8
α-helix	714-722	9
β-strand	729	1	36
α-helix	734-742	9
β-strand	747-749	3	36
β-strand	756-758	3	35
β-strand	761-762	2	31
α-helix	769-782	14
α-helix	784-792	9
α-helix	802-806	5
β-strand	808	1	23
α-helix	810-839	30

Chain D: 31 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	38
α-helix	48-55	8
β-strand	67-73	7	38
α-helix	78-92	15
β-strand	96-100	5	38
α-helix	107-118	12
β-strand	123-127	5	38
α-helix	128-131	4
β-strand	143-145	3	38
α-helix	150-161	12
β-strand	170-171	2	39
β-strand	174	1	40
α-helix	179-191	13
β-strand	201-202	2	39
β-strand	205	1	40
α-helix	213-221	9
β-strand	227-229	3	39
α-helix	234-243	10
β-strand	255-258	4	39
α-helix	274	1
β-strand	278-282	5	39
α-helix	289-311	23
α-helix	335-339	5
β-strand	343-344	2	41
β-strand	347-348	2	41
β-strand	351	1	42
β-strand	357	1	42
β-strand	362-367	6	39
β-strand	373-379	7	39
β-strand	380	1	43
β-strand	383	1	43
β-strand	386	1	39
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	434-437	4	44
β-strand	454-458	5	44
α-helix	460-472	13
β-strand	475-480	6	44
β-strand	490	1	46
β-strand	493	1	46
α-helix	496-502	7
β-strand	508-514	7	44
α-helix	518-521	4
β-strand	524-525	2	44
β-strand	530-539	10	44
β-strand	541	1	47
α-helix	549-551	3
β-strand	554	1	12
α-helix	556-579	24
α-helix	602-613	12
α-helix	620-622	3
α-helix	627-653	27
β-strand	656-657	2	48
β-strand	659	1	47
α-helix	669-672	4
α-helix	674-676	3
β-strand	683-684	2	44
α-helix	690-698	9
α-helix	701-706	6
α-helix	714-723	10
β-strand	728-732	5	44
α-helix	733-740	8
β-strand	748-750	3	44
α-helix	753-755	3
β-strand	757-766	10	44
α-helix	773-786	14
α-helix	788-796	9
α-helix	804-807	4
β-strand	808-809	2	48
β-strand	813	1	37
α-helix	821-839	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	814	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	808	Homo sapiens	Q13224 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9IYP_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
VNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQ
VYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSH
QSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTA
LLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGI
LGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLM
SSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGET
EKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTSPGS
PRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELL
SGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLV
GLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRS
FSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQ
SSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDL
VTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPA
TLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH

Sequence of entity 2 (B, D), FASTA

>9IYP_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
IGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKI
QGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQA
SVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDS
KIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFP
TGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNM
LNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRM
CPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIK
KCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLT
INEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAV
FVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSV
WAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERN
IRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSG
KVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLD
IDNMAGVFYMLGAAMALSLITFICEHLF

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	3
7RC	(2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid	C8 H17 N2 O5 P	2
MG	Magnesium ion	Mg	7

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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