7YFL: GluN1a-GluN2D NMDA receptor

Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Determined by electron microscopy at 3.9 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 19,968
Mol. weight: 389.28 kDa
Ligands: GLU, NAG, GLY
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

7YFL contains 118 α-helices and 144 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: 31 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	1
α-helix	38-50	13
β-strand	66	1	1
α-helix	73-80	8
α-helix	81-85	5
β-strand	90-92	3	2
α-helix	104-114	11
β-strand	118-120	3	2
α-helix	126-129	4
β-strand	138-139	2	2
α-helix	144-146	3
α-helix	147-158	12
β-strand	164-168	5	3
α-helix	171-186	16
β-strand	195-197	3	3
α-helix	205-209	5
β-strand	216	1	4
β-strand	219-222	4	3
α-helix	225-238	14
β-strand	247-249	3	3
α-helix	252-254	3
α-helix	256-259	4
β-strand	270	1	5
α-helix	277-295	19
α-helix	317-327	11
β-strand	340	1	6
β-strand	345	1	2
β-strand	346	1	6
β-strand	350	1	7
β-strand	352	1	5
β-strand	368	1	7
β-strand	392	1	4
β-strand	397-402	6	8
β-strand	405	1	8
β-strand	409-412	4	8
α-helix	420-422	3
β-strand	424	1	9
β-strand	430	1	9
β-strand	433-439	7	8
β-strand	450-457	8	8
α-helix	458-470	13
β-strand	473-478	6	8
β-strand	485-489	5	10
β-strand	496-500	5	10
α-helix	501-506	6
β-strand	512-513	2	8
α-helix	521-524	4
β-strand	527-529	3	8
α-helix	530-532	3
β-strand	538-543	6	11
α-helix	544-546	3
α-helix	555-579	25
α-helix	605-612	8
α-helix	629-655	27
α-helix	670-673	4
β-strand	676	1	12
β-strand	679	1	12
β-strand	681-682	2	11
α-helix	688-692	5
α-helix	697-699	3
α-helix	700-708	9
α-helix	715-722	8
β-strand	728-732	5	11
α-helix	733-743	11
β-strand	746-753	8	11
β-strand	761-763	3	8
α-helix	768-782	15
α-helix	784-792	9

Chains B and D: 28 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	64-69	6
α-helix	71-75	5
α-helix	96-110	15
α-helix	127-136	10
β-strand	141-142	2	13
β-strand	161-162	2	13
α-helix	168-178	11
β-strand	185	1	14
β-strand	188	1	15
β-strand	191	1	16
α-helix	197-207	11
β-strand	214	1	14
β-strand	220	1	16
α-helix	230-238	9
β-strand	243-246	4	15
β-strand	247	1	16
α-helix	250-262	13
β-strand	271-274	4	15
α-helix	299-301	3
β-strand	304-309	6	15
α-helix	310-312	3
α-helix	316-337	22
α-helix	362-364	3
β-strand	367-369	3	17
β-strand	372-374	3	17
β-strand	387-392	6	15
β-strand	398-405	8	15
β-strand	408-410	3	15
β-strand	433-434	2	18
β-strand	439	1	18
β-strand	443-447	5	18
β-strand	460-463	4	18
β-strand	482-486	5	18
α-helix	488-495	8
α-helix	496-500	5
β-strand	504-506	3	18
β-strand	517	1	19
β-strand	520	1	19
α-helix	523-529	7
β-strand	535	1	18
β-strand	541	1	20
α-helix	544-549	6
β-strand	551	1	21
β-strand	558-561	4	22
β-strand	562-565	4	23
α-helix	583-592	10
α-helix	637-641	5
α-helix	655-681	27
α-helix	696-699	4
α-helix	706-707	2
β-strand	711	1	23
α-helix	718-725	8
α-helix	731-733	3
α-helix	742-749	8
β-strand	755-758	4	23
α-helix	762-765	4
β-strand	775-776	2	23
β-strand	784-788	5	22
β-strand	789	1	20
β-strand	793	1	21
α-helix	800-812	13
α-helix	815-823	9
α-helix	841-852	12

Chain C: 31 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	24
α-helix	38-51	14
β-strand	66	1	24
α-helix	73-80	8
α-helix	81-85	5
β-strand	90-92	3	25
α-helix	104-114	11
β-strand	118-120	3	25
α-helix	126-129	4
β-strand	138-139	2	25
α-helix	144-146	3
α-helix	147-158	12
β-strand	164-168	5	26
α-helix	171-186	16
β-strand	195-197	3	26
α-helix	205-209	5
β-strand	216	1	27
β-strand	219-222	4	26
α-helix	225-238	14
β-strand	247-249	3	26
α-helix	252-254	3
α-helix	256-259	4
β-strand	270	1	28
α-helix	277-295	19
α-helix	317-327	11
β-strand	340	1	29
β-strand	345	1	25
β-strand	346	1	29
β-strand	350	1	30
β-strand	352	1	28
β-strand	368	1	30
β-strand	392	1	27
β-strand	397-402	6	31
β-strand	405	1	31
β-strand	409-412	4	31
α-helix	420-422	3
β-strand	424	1	32
β-strand	430	1	32
β-strand	433-439	7	31
β-strand	450-457	8	31
α-helix	458-470	13
β-strand	473-478	6	31
β-strand	485-489	5	33
β-strand	496-500	5	33
α-helix	501-506	6
β-strand	512-513	2	31
α-helix	521-524	4
β-strand	527-529	3	31
α-helix	530-532	3
β-strand	538-543	6	34
α-helix	544-546	3
α-helix	559-579	21
α-helix	605-612	8
α-helix	629-655	27
α-helix	670-673	4
β-strand	676	1	35
β-strand	679	1	35
β-strand	681-682	2	34
α-helix	688-692	5
α-helix	697-699	3
α-helix	700-708	9
α-helix	715-722	8
β-strand	728-732	5	34
α-helix	733-743	11
β-strand	746-753	8	34
β-strand	761-763	3	31
α-helix	768-782	15
α-helix	784-792	9

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

>7YFL_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

>7YFL_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
GLU	Glutamic acid	C5 H9 N O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
GLY	Glycine	C2 H5 N O2	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

About this viewer

MolViewer shows 7YFL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.