8VUL: Glutamate receptor ionotropic, NMDA 1

Human GluN1-2A with Fab 003-102 Local refinement of ATD. Determined by electron microscopy at 3.83 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.83 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,158
Mol. weight: 107.1 kDa
Released: 11 Sept 2024

Explore 8VUL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VUL contains 27 α-helices and 62 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: 15 helices, 15 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	72-85	14
β-strand	90-92	3	1
α-helix	105-113	9
β-strand	118-119	2	1
α-helix	126-129	4
β-strand	138	1	1
α-helix	142-143	2
α-helix	144-146	3
α-helix	148-158	11
β-strand	163-168	6	2
α-helix	171-185	15
β-strand	193-197	5	2
α-helix	205-212	8
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-248	3	2
α-helix	257-259	3
α-helix	262-263	2
β-strand	267-271	5	2
α-helix	278-295	18
α-helix	303-305	3
α-helix	318-326	9
β-strand	340	1	3
β-strand	346	1	3
β-strand	351-356	6	2
β-strand	361-367	7	2
β-strand	372-374	3	2

Chain B: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	4
α-helix	51-54	4
β-strand	68-70	3	4
β-strand	73	1	4
α-helix	79-93	15
β-strand	98-101	4	4
β-strand	102	1	5
α-helix	108-120	13
β-strand	124	1	4
β-strand	129	1	5
α-helix	130-132	3
β-strand	144	1	4
α-helix	151-164	14
β-strand	172	1	6
β-strand	173	1	7
α-helix	180-192	13
β-strand	204	1	7
α-helix	215-220	6
β-strand	227-228	2	6
α-helix	233-246	14
β-strand	255-257	3	6
β-strand	277-280	4	6
α-helix	288-309	22
α-helix	313-317	5
β-strand	342	1	8
β-strand	347	1	8
β-strand	350	1	9
β-strand	356	1	9
β-strand	362-367	6	6
β-strand	371-378	8	6
β-strand	383-385	3	6

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	12	1	11
β-strand	20-25	6	10
β-strand	33-40	8	12
β-strand	47-53	7	12
β-strand	58-60	3	12
α-helix	62-67	6
β-strand	71-73	3	10
β-strand	78-81	4	10
β-strand	92-100	9	12
β-strand	107-110	4	12
β-strand	114-116	3	12
β-strand	118	1	11

Chain L: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	10-11	2	14
β-strand	18	1	15
β-strand	23-24	2	13
β-strand	34-39	6	12
β-strand	46-49	4	12
β-strand	63-64	2	15
β-strand	67	1	16
β-strand	74	1	16
β-strand	77-78	2	15
α-helix	83-85	3
β-strand	88-94	7	12
β-strand	99-100	2	12
β-strand	106	1	12
β-strand	107-108	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A	protein	369	Homo sapiens	Q05586 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B	protein	366	Homo sapiens	Q12879 (AlphaFold model)
003-102 Heavy	H	protein	119	Homo sapiens
003-102 Light	L	protein	109	Homo sapiens

Sequence of entity 1 (A), FASTA

>8VUL_1 Glutamate receptor ionotropic, NMDA 1 (chains A)
KIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLIS
SQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPY
SHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNV
TALLMEAKELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPD
GILGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRV
LMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGG
ETEKPRGYQ

Sequence of entity 2 (B), FASTA

>8VUL_2 Glutamate receptor ionotropic, NMDA 2A (chains B)
LNIAVMLGHSHDVTERELRTLWGPEQAAGLPLDVNVVALLMNRTDPKSLITHVCDLMSGA
RIHGLVFGDDTDQEAVAQMLDFISSHTFVPILGIHGGASMIMADKDPTSTFFQFGASIQQ
QATVMLKIMQDYDWHVFSLVTTIFPGYREFISFVKTTVDNSFVGWDMQNVITLDTSFEDA
KTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFP
SGLISVSYDDWDYSLEARVRDGIGILTTAASSMLEKFSYIPEAKASCYGQMERPEVPMHT
LHPFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENHTLSLRHAVWPRY
KSFSDC

Sequence of entity 3 (H), FASTA

>8VUL_3 003-102 Heavy (chains H)
LQLQESGPGLVKPSQTLSLTCTVSGGSISSSNWWSWVRQPPGKGLEWIGEIYHSGNTNYN
PSLKSRVTVSVDKSKNQFSLKLTSVTAADTAVYYCARDVSGGVNWFDPWGQGTLVTVSS

Sequence of entity 4 (L), FASTA

>8VUL_4 003-102 Light (chains L)
NFMLTQPHSVSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSAPTTVIYEDNQRPSGVP
DRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSTVVFGGGTKLTV

Primary citation

Structural and functional mechanisms of anti-NMDAR autoimmune encephalitis. Michalski, K., Abdulla, T., Kleeman, S. et al. Nat Struct Mol Biol (2024) 31:1975-1986. DOI 10.1038/s41594-024-01386-4 · 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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