8BHK: GABA-A receptor a5 homomer - a5V3 - Diazepam

GABA-A receptor a5 homomer - a5V3 - Diazepam. Determined by electron microscopy at 3.3 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,750
Mol. weight: 207.82 kDa
Ligands: DZP, NAG
Released: 1 Nov 2023

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

Secondary structure: helices and β-sheets

8BHK contains 65 α-helices and 80 β-strands across 5 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.

Chains A, B, C, D and E: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
β-strand	42-57	16	1
β-strand	62-73	12	1
β-strand	74	1	2
α-helix	76-78	3
α-helix	91-93	3
β-strand	102-104	3	3
β-strand	107-111	5	1
β-strand	120	1	1
β-strand	123-124	2	4
β-strand	129	1	2
β-strand	130-131	2	4
β-strand	132-141	10	1
β-strand	153-162	10	3
β-strand	170-174	5	1
α-helix	178-181	4
β-strand	182-184	3	1
α-helix	186-188	3
β-strand	189	1	1
β-strand	195-207	13	3
β-strand	212-223	12	3
α-helix	224-226	3
α-helix	228-229	2
α-helix	230-234	5
α-helix	235-245	11
α-helix	246-249	4
α-helix	255-279	25
α-helix	288-312	25
α-helix	318-417	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit alpha-5	A, B, C, D, E	protein	360	Homo sapiens	P31644 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>8BHK_1 Gamma-aminobutyric acid receptor subunit alpha-5 (chains A, B, C, D, E)
QMPTSSVKDETNDNITIFTRILDGLLDGYDNRLRPGLGERITQVRTDMYVNSFGPVSDTE
MEYTIDIFFAQTWKDERLRFKGPMQRLPLNNLLASKIWTPDTFFHNGKKSFAHWMTTPNR
MLRIWNDGRVLYTLRLTISAECPMDLEDFPMDEQNCPLKFGSYAYPNSEVVYVWTNGSTK
SVVVAEDGSRLNQYHLMGQTVGTENISTSTGEYTIMTAHFHLKRKIGYFVIQTYLPCIMT
VILSQVSFWLNRESVAARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFV
FSALLEFAFVNYITKSQPARAAKIDKMSRIVFPILFGTFNLVYWATYLNGTTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
DZP	7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one	C16 H13 Cl N2 O	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

The molecular basis of drug selectivity for alpha 5 subunit-containing GABA A receptors. Kasaragod, V.B., Malinauskas, T., Wahid, A.A. et al. Nat Struct Mol Biol (2023) 30:1936-1946. DOI 10.1038/s41594-023-01133-1 · PubMed

Other PDB entries of the same protein (UniProt P31644 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8BHG 2.39 Å, GABA-A receptor a5 heteromer - a5V2 - Bretazenil
8BHB 2.54 Å, GABA-A receptor a5 homomer - a5V3 - RO154513
8BGI 2.56 Å, GABA-A receptor a5 homomer - a5V1 - Flumazenil
8BHA 2.67 Å, GABA-A receptor a5 homomer - a5V3 - Basmisanil - HR
8BHI 2.67 Å, GABA-A receptor a5 homomer - a5V3 - RO5211223
8BHO 2.93 Å, GABA-A receptor a5 homomer - a5V3 - L655708
8BHM 2.95 Å, GABA-A receptor a5 homomer - a5V3 - DMCM
9HNS 3.1 Å, a5b3 GABAAR bound to GABA and Mb25 in a desensitized state in saposin nanodiscs after…
9RL5 3.1 Å, a5b3 GABAAR bound to Topiramate, GABA, and Mb25 in a desensitized state in saposin…
9RPB 3.1 Å, a5b3 GABAAR bound to GABA, and Mb25 in a desensitized state in saposin nanodiscs,…
9HAA 3.14 Å, a5b3 GABAA Receptor resting state
9HNR 3.17 Å, a5b3 GABAA Receptor in 1 a5 to 4 b3 stoichiometry in desensitized state

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