7YFF: GluN1a-GluN2D NMDA receptor

Structure of GluN1a-GluN2D NMDA receptor in complex with agonist glycine and competitive antagonist CPP. Determined by electron microscopy at 3.6 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 21,820
Mol. weight: 386.63 kDa
Ligands: 7RC, GLY, NAG
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

7YFF contains 140 α-helices and 139 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: 38 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	39-52	14
α-helix	71-85	15
β-strand	91-92	2	1
α-helix	105-112	8
α-helix	113-115	3
β-strand	118-120	3	1
α-helix	126-128	3
β-strand	137-139	3	1
α-helix	142-143	2
α-helix	145-157	13
β-strand	164-167	4	2
α-helix	171-186	16
β-strand	193	1	2
α-helix	205-212	8
β-strand	219-222	4	2
α-helix	225-237	13
β-strand	247-249	3	2
α-helix	251-260	10
β-strand	266-271	6	2
α-helix	274-277	4
α-helix	281-294	14
α-helix	303-305	3
α-helix	313-315	3
α-helix	318-327	10
β-strand	340-341	2	3
β-strand	345-346	2	3
β-strand	351-355	5	2
α-helix	357-359	3
β-strand	362-367	6	2
β-strand	372-373	2	2
α-helix	378-379	2
α-helix	388-390	3
β-strand	399-402	4	4
β-strand	405	1	4
β-strand	409-413	5	4
α-helix	420-422	3
β-strand	424	1	5
β-strand	430	1	5
β-strand	434-438	5	4
β-strand	451-457	7	4
α-helix	458-470	13
β-strand	475-478	4	4
β-strand	486-490	5	6
β-strand	493-499	7	6
α-helix	501-507	7
β-strand	512	1	4
β-strand	516	1	7
α-helix	517-519	3
α-helix	521-526	6
β-strand	528	1	4
α-helix	530-532	3
β-strand	535-536	2	8
β-strand	538-543	6	9
α-helix	560-583	24
α-helix	603-615	13
α-helix	627-657	31
α-helix	660-662	3
α-helix	670-673	4
β-strand	681-682	2	9
β-strand	684	1	10
α-helix	688-695	8
α-helix	700-709	10
β-strand	711	1	10
α-helix	714-723	10
β-strand	728-732	5	9
α-helix	733-742	10
β-strand	746-749	4	9
β-strand	756-757	2	8
β-strand	759	1	7
β-strand	762	1	4
α-helix	769-775	7
α-helix	776-784	9
α-helix	785-792	8
α-helix	812-839	28

Chain B: 32 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	61-67	7
α-helix	68-72	5
α-helix	73-74	2
α-helix	96-109	14
β-strand	117-118	2	11
α-helix	126-137	12
β-strand	143-144	2	11
β-strand	163	1	11
α-helix	168-181	14
β-strand	191	1	12
α-helix	198-208	11
α-helix	230-237	8
β-strand	244-246	3	13
β-strand	247	1	12
α-helix	250-263	14
β-strand	271-274	4	13
β-strand	303-309	7	13
α-helix	316-334	19
β-strand	376	1	14
β-strand	382	1	14
β-strand	387-392	6	13
β-strand	398-405	8	13
β-strand	408-411	4	13
β-strand	431-436	6	15
β-strand	439	1	16
β-strand	443-447	5	16
α-helix	448-449	2
α-helix	455-456	2
β-strand	460-462	3	16
β-strand	482-486	5	16
α-helix	487-495	9
α-helix	496-500	5
β-strand	502-507	6	15
β-strand	515-517	3	17
β-strand	520-522	3	17
α-helix	524-528	5
β-strand	541	1	18
α-helix	544-549	6
β-strand	551	1	19
β-strand	557-559	3	18
β-strand	561-565	5	20
β-strand	568	1	21
α-helix	571-573	3
α-helix	575-578	4
α-helix	583-606	24
α-helix	631-640	10
α-helix	655-680	26
β-strand	682-684	3	22
β-strand	686	1	21
α-helix	706-707	2
α-helix	709-710	2
β-strand	711	1	20
α-helix	718-725	8
α-helix	727-733	7
α-helix	742-747	6
β-strand	755-759	5	20
α-helix	760-769	10
β-strand	776-777	2	20
β-strand	787-789	3	18
β-strand	793	1	19
α-helix	794	1
α-helix	800-813	14
α-helix	816-820	5
α-helix	821-823	3
β-strand	834-836	3	22
α-helix	842-868	27

Chain C: 38 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	39-52	14
α-helix	71-85	15
β-strand	91-92	2	23
α-helix	105-112	8
α-helix	113-115	3
β-strand	118-120	3	23
α-helix	126-128	3
β-strand	137-139	3	23
α-helix	142-143	2
α-helix	145-157	13
β-strand	164-167	4	24
α-helix	171-186	16
α-helix	205-212	8
β-strand	219-222	4	24
α-helix	225-237	13
β-strand	247-249	3	24
α-helix	251-260	10
β-strand	266-271	6	24
α-helix	274-277	4
α-helix	281-294	14
α-helix	303-305	3
α-helix	313-315	3
α-helix	318-327	10
β-strand	340-341	2	25
β-strand	345-346	2	25
β-strand	351-355	5	24
α-helix	357-359	3
β-strand	362-367	6	24
β-strand	372-373	2	24
α-helix	378-379	2
α-helix	388-390	3
β-strand	399-402	4	26
β-strand	405	1	26
β-strand	409-413	5	26
α-helix	420-422	3
β-strand	424	1	27
β-strand	430	1	27
β-strand	434-438	5	26
β-strand	451-457	7	26
α-helix	458-470	13
β-strand	475-478	4	26
β-strand	486-490	5	28
β-strand	493-499	7	28
α-helix	501-507	7
β-strand	512	1	26
β-strand	515-516	2	29
α-helix	517-519	3
α-helix	521-526	6
β-strand	528	1	30
α-helix	530-532	3
β-strand	535-536	2	31
β-strand	538-543	6	32
α-helix	560-583	24
α-helix	603-615	13
α-helix	627-657	31
α-helix	660-662	3
α-helix	670-673	4
β-strand	681-682	2	32
β-strand	684	1	33
α-helix	688-695	8
α-helix	700-709	10
β-strand	711	1	33
α-helix	714-723	10
β-strand	728-732	5	32
α-helix	733-742	10
β-strand	746-749	4	32
β-strand	756-757	2	31
β-strand	759	1	29
β-strand	762	1	30
α-helix	769-775	7
α-helix	776-784	9
α-helix	785-792	8
α-helix	812-839	28

Chain D: 32 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	61-67	7
α-helix	68-72	5
α-helix	73-74	2
α-helix	96-109	14
β-strand	117-118	2	34
α-helix	126-137	12
β-strand	143-144	2	34
β-strand	163	1	34
α-helix	168-181	14
β-strand	191	1	35
α-helix	198-208	11
α-helix	230-237	8
β-strand	244-246	3	36
β-strand	247	1	35
α-helix	250-263	14
β-strand	271-274	4	36
β-strand	303-309	7	36
α-helix	316-334	19
β-strand	376	1	37
β-strand	382	1	37
β-strand	387-392	6	36
β-strand	398-405	8	36
β-strand	408-411	4	36
β-strand	431-436	6	38
β-strand	439	1	39
β-strand	443-447	5	39
α-helix	448-449	2
α-helix	455-456	2
β-strand	460-462	3	39
β-strand	482-486	5	39
α-helix	487-495	9
α-helix	496-500	5
β-strand	502-507	6	38
β-strand	515-517	3	40
β-strand	520-522	3	40
α-helix	524-528	5
β-strand	541	1	41
α-helix	544-549	6
β-strand	551	1	42
β-strand	557-559	3	41
β-strand	561-565	5	43
β-strand	568	1	44
α-helix	571-573	3
α-helix	575-578	4
α-helix	583-606	24
α-helix	631-640	10
α-helix	655-680	26
β-strand	682-683	2	45
β-strand	686	1	44
α-helix	706-707	2
α-helix	709-710	2
β-strand	711	1	43
α-helix	718-725	8
α-helix	727-733	7
α-helix	742-747	6
β-strand	755-759	5	43
α-helix	760-769	10
β-strand	776-777	2	43
β-strand	787-789	3	41
β-strand	793	1	42
α-helix	794	1
α-helix	800-813	14
α-helix	816-820	5
α-helix	821-823	3
β-strand	835-836	2	45
α-helix	842-868	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	840	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

>7YFF_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNM
TGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA
DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH

Sequence of entity 2 (B, D), FASTA

>7YFF_2 Glutamate receptor ionotropic, NMDA 2D (chains B, D)
MRGAGGPRGPRGPAKMLLLLALACASPFPEEAPGPGGAGGPGGGLGGARPLNVALVFSGP
AYAAEAARLGPAVAAAVRSPGLDVRPVALVLNGSDPRSLVLQLCDLLSGLRVHGVVFEDD
SRAPAVAPILDFLSAQTSLPIVAVHGGAALVLTPKEKGSTFLQLGSSTEQQLQVIFEVLE
EYDWTSFVAVTTRAPGHRAFLSYIEVLTDGSLVGWEHRGALTLDPGAGEAVLSAQLRSVS
AQIRLLFCAREEAEPVFRAAEEAGLTGSGYVWFMVGPQLAGGGGSGAPGEPPLLPGGAPL
PAGLFAVRSAGWRDDLARRVAAGVAVVARGAQALLRDYGFLPELGHDCRAQNRTHRGESL
HRYFMNITWDNRDYSFNEDGFLVNPSLVVISLTRDRTWEVVGSWEQQTLRLKYPLWSRYG
RFLQPVDDTQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPE
KRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSL
TINEERSEIVDFSVPFVETGISVMVARSNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVT
VFIFEYLSPVGYNRSLATGKRPGGSTFTIGKSIWLLWALVFNNSVPVENPRGTTSKIMVL
VWAFFAVIFLASYTANLAAFMIQEEYVDTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEK
NIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGS
GKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICHNDKIEVMSSKL
DIDNMAGVFYMLLVAMGLSLLVFAWEHLVYWRLRHCLGPAASAWSHPQFEK

Ligands and cofactors

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

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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