7YFR: Glutamate receptor ionotropic, NMDA 1

Structure of GluN1a E698C-GluN2D NMDA receptor in cystines non-crosslinked state. Determined by electron microscopy at 5.1 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 5.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 19,142
Mol. weight: 389.32 kDa
Ligands: GLY, NAG, GLU
Released: 12 Apr 2023

Explore 7YFR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YFR contains 100 α-helices and 146 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: 27 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	38-51	14
α-helix	71-84	14
β-strand	91-92	2	1
α-helix	105-114	10
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-157	14
β-strand	164-168	5	2
α-helix	171-183	13
β-strand	193-197	5	2
α-helix	205-213	9
β-strand	219-222	4	2
α-helix	225-237	13
β-strand	247-249	3	2
α-helix	251-260	10
β-strand	267-271	5	2
α-helix	277-295	19
α-helix	317-327	11
β-strand	329	1	3
β-strand	339-340	2	3
β-strand	346-347	2	3
β-strand	351-356	6	2
β-strand	361-367	7	2
β-strand	372	1	2
β-strand	397-402	6	4
β-strand	405	1	5
β-strand	409	1	5
β-strand	410-413	4	6
β-strand	424	1	7
β-strand	430	1	7
β-strand	434-436	3	6
β-strand	437	1	4
β-strand	453-456	4	6
α-helix	458-469	12
β-strand	473-478	6	4
β-strand	487-489	3	8
α-helix	490	1
β-strand	496-498	3	8
α-helix	500-502	3
α-helix	503-506	4
β-strand	512-518	7	4
α-helix	519	1
α-helix	521-526	6
β-strand	528	1	4
β-strand	538-543	6	9
α-helix	558-561	4
α-helix	602-610	9
α-helix	628-656	29
α-helix	670-673	4
β-strand	681-682	2	9
β-strand	684	1	10
α-helix	688-695	8
α-helix	698-706	9
β-strand	711	1	10
α-helix	714-722	9
β-strand	728-732	5	9
α-helix	733-742	10
β-strand	746-749	4	9
β-strand	758-762	5	4
α-helix	768-781	14
α-helix	783-790	8

Chain B: 23 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	52-57	6	11
α-helix	62-76	15
β-strand	87	1	11
α-helix	96-109	14
β-strand	112-118	7	11
α-helix	123-137	15
β-strand	141-144	4	11
α-helix	168-178	11
β-strand	185	1	12
β-strand	188-191	4	13
α-helix	197-207	11
β-strand	214	1	12
β-strand	217-220	4	13
α-helix	229-237	9
β-strand	243-247	5	13
α-helix	250-263	14
β-strand	271-274	4	13
β-strand	304-308	5	13
α-helix	316-337	22
β-strand	368-369	2	14
β-strand	372-373	2	14
β-strand	376	1	15
β-strand	382	1	15
β-strand	387-392	6	13
β-strand	398-405	8	13
β-strand	408-411	4	13
β-strand	431-435	5	16
β-strand	439	1	16
β-strand	443-447	5	16
α-helix	448	1
β-strand	449	1	17
β-strand	454	1	17
α-helix	455-456	2
β-strand	460-463	4	16
β-strand	481-486	6	16
α-helix	487-499	13
β-strand	502-506	5	16
β-strand	517	1	18
β-strand	520	1	18
α-helix	523-529	7
β-strand	535-536	2	16
β-strand	541	1	19
α-helix	544-549	6
β-strand	561-567	7	20
α-helix	662-681	20
α-helix	696-699	4
β-strand	710-711	2	20
α-helix	717-725	9
α-helix	727-732	6
α-helix	741-750	10
β-strand	755-759	5	20
α-helix	760-769	10
β-strand	774-776	3	20
α-helix	778-780	3
β-strand	784	1	20
β-strand	789	1	19
β-strand	793	1	16
α-helix	800-811	12
α-helix	815-823	9
α-helix	839-849	11

Chain C: 27 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	38-51	14
α-helix	71-84	14
β-strand	91-92	2	21
α-helix	105-114	10
β-strand	118-120	3	21
α-helix	126-129	4
β-strand	137-139	3	21
α-helix	144-157	14
β-strand	164-168	5	22
α-helix	171-183	13
β-strand	193-197	5	22
α-helix	206-213	8
β-strand	216	1	23
β-strand	219-222	4	22
α-helix	225-237	13
β-strand	247-249	3	22
α-helix	251-260	10
β-strand	267-271	5	22
α-helix	277-295	19
α-helix	317-327	11
β-strand	329	1	24
β-strand	339-340	2	24
β-strand	346-347	2	24
β-strand	351-356	6	22
β-strand	361-367	7	22
β-strand	372	1	22
β-strand	392	1	23
β-strand	397-402	6	25
β-strand	405	1	26
β-strand	409	1	26
β-strand	410-413	4	27
β-strand	424	1	28
β-strand	430	1	28
β-strand	434-436	3	27
β-strand	437	1	25
β-strand	453-456	4	27
α-helix	458-469	12
β-strand	473-478	6	25
β-strand	487-489	3	29
α-helix	490	1
β-strand	496-498	3	29
α-helix	500-502	3
α-helix	503-506	4
β-strand	512-518	7	25
α-helix	519	1
α-helix	521-526	6
β-strand	528	1	25
β-strand	538-543	6	30
α-helix	558-561	4
α-helix	602-610	9
α-helix	628-656	29
α-helix	670-673	4
β-strand	681-682	2	30
β-strand	684	1	31
α-helix	688-695	8
α-helix	698-706	9
β-strand	711	1	31
α-helix	714-722	9
β-strand	728-732	5	30
α-helix	733-742	10
β-strand	746-749	4	30
β-strand	758-762	5	25
α-helix	768-781	14
α-helix	783-790	8

Chain D: 23 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	52-57	6	32
α-helix	62-76	15
β-strand	87	1	32
α-helix	96-109	14
β-strand	112-118	7	32
α-helix	123-137	15
β-strand	141-144	4	32
α-helix	168-178	11
β-strand	185	1	33
β-strand	188-191	4	34
α-helix	197-207	11
β-strand	214	1	33
β-strand	217-220	4	34
α-helix	229-237	9
β-strand	243-247	5	34
α-helix	250-263	14
β-strand	271-274	4	34
β-strand	304-308	5	34
α-helix	316-337	22
β-strand	368-369	2	35
β-strand	372-373	2	35
β-strand	376	1	36
β-strand	382	1	36
β-strand	387-392	6	34
β-strand	398-405	8	34
β-strand	408-411	4	34
β-strand	431-435	5	37
β-strand	439	1	37
β-strand	443-447	5	37
α-helix	448	1
β-strand	449	1	38
β-strand	454	1	38
α-helix	455-456	2
β-strand	460-463	4	37
β-strand	481-486	6	37
α-helix	487-499	13
β-strand	502-506	5	37
β-strand	517	1	39
β-strand	520	1	39
α-helix	523-529	7
β-strand	535-536	2	37
β-strand	541	1	40
α-helix	544-549	6
β-strand	561-567	7	41
α-helix	662-682	21
α-helix	696-699	4
β-strand	710-711	2	41
α-helix	717-725	9
α-helix	727-732	6
α-helix	741-750	10
β-strand	755-759	5	41
α-helix	760-769	10
β-strand	774-776	3	41
α-helix	778-780	3
β-strand	784	1	41
β-strand	789	1	40
β-strand	793	1	37
α-helix	800-811	12
α-helix	815-823	9
α-helix	839-849	11

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 2D	B, D	protein	891	Homo sapiens	O15399 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7YFR_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNM
TGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA
DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVCLSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDARRKQ

Sequence of entity 2 (B, D), FASTA

>7YFR_2 Glutamate receptor ionotropic, NMDA 2D (chains B, D)
MRGAGGPRGPRGPAKMLLLLALACASPFPEEAPGPGGAGGPGGGLGGARPLNVALVFSGP
AYAAEAARLGPAVAAAVRSPGLDVRPVALVLNGSDPRSLVLQLCDLLSGLRVHGVVFEDD
SRAPAVAPILDFLSAQTSLPIVAVHGGAALVLTPKEKGSTFLQLGSSTEQQLQVIFEVLE
EYDWTSFVAVTTRAPGHRAFLSYIEVLTDGSLVGWEHRGALTLDPGAGEAVLSAQLRSVS
AQIRLLFCAREEAEPVFRAAEEAGLTGSGYVWFMVGPQLAGGGGSGAPGEPPLLPGGAPL
PAGLFAVRSAGWRDDLARRVAAGVAVVARGAQALLRDYGFLPELGHDCRAQNRTHRGESL
HRYFMNITWDNRDYSFNEDGFLVNPSLVVISLTRDRTWEVVGSWEQQTLRLKYPLWSRYG
RFLQPVDDTQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPE
KRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSL
TINEERSEIVDFSVPFVETGISVMVARSNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVT
VFIFEYLSPVGYNRSLATGKRPGGSTFTIGKSIWLLWALVFNNSVPVENPRGTTSKIMVL
VFAFFAVIFLASYTANLAAFMIQEEYVDTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEK
NIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGS
GKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICHNDKIEVMSSKL
DIDNMAGVFYMLLVAMGLSLLVFAWEHLVYWRLRHCLGPAASAWSHPQFEK

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	5
GLU	Glutamic acid	C5 H9 N O4	2

Primary citation

Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits. Zhang, J., Zhang, M., Wang, Q. et al. Nat Struct Mol Biol (2023) 30:629-639. DOI 10.1038/s41594-023-00959-z · 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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