8BGI: GABA-A receptor a5 homomer - a5V1 - Flumazenil

GABA-A receptor a5 homomer - a5V1 - Flumazenil. Determined by X-ray diffraction at 2.56 Å resolution. Released 8 Nov 2023.

Method: X-ray diffraction
Resolution: 2.56 Å
Organism: Homo sapiens
Chains: 5
Atoms: 14,002
Mol. weight: 213.25 kDa
Ligands: NAG, P9N, FYP
Released: 8 Nov 2023

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

Secondary structure: helices and β-sheets

8BGI contains 55 α-helices and 65 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.

Chain A: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	34	1
β-strand	42-57	16	1
β-strand	62-74	13	1
α-helix	76-78	3
β-strand	86-89	4	1
α-helix	91-94	4
β-strand	102-104	3	2
β-strand	107-112	6	1
β-strand	120-125	6	1
β-strand	129-141	13	1
β-strand	153-156	4	2
β-strand	159-162	4	2
β-strand	170-174	5	1
β-strand	182-184	3	1
β-strand	194-209	16	2
β-strand	211-224	14	2
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-244	10
α-helix	247-249	3
α-helix	255-278	24
α-helix	288-314	27
α-helix	318-417	30

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	34	1
β-strand	42-57	16	3
β-strand	62-74	13	3
α-helix	76-78	3
β-strand	86-89	4	3
α-helix	91-94	4
β-strand	102-104	3	4
β-strand	107-112	6	3
β-strand	120-125	6	3
β-strand	129-141	13	3
β-strand	153-162	10	4
β-strand	170-174	5	3
β-strand	182-184	3	3
β-strand	194-209	16	4
β-strand	211-224	14	4
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-244	10
α-helix	245-249	5
α-helix	255-279	25
α-helix	288-314	27
α-helix	318-417	30

Chain C: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	34	1
β-strand	42-57	16	5
β-strand	62-74	13	5
α-helix	76-78	3
β-strand	86-89	4	5
α-helix	91-94	4
β-strand	102-104	3	6
β-strand	107-112	6	5
β-strand	120-125	6	5
β-strand	129-141	13	5
β-strand	153-156	4	6
β-strand	159-162	4	6
β-strand	170-174	5	5
β-strand	182-184	3	5
β-strand	194-209	16	6
β-strand	211-224	14	6
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-244	10
α-helix	245-249	5
α-helix	255-279	25
α-helix	288-313	26
α-helix	318-417	30

Chain D: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	34	1
β-strand	42-57	16	7
β-strand	62-74	13	7
α-helix	76-78	3
β-strand	86-89	4	7
α-helix	91-94	4
β-strand	102-104	3	8
β-strand	107-112	6	7
β-strand	120-125	6	7
β-strand	129-141	13	7
β-strand	153-156	4	8
β-strand	159-162	4	8
β-strand	170-174	5	7
β-strand	182-188	7	7
β-strand	194-209	16	8
β-strand	211-224	14	8
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-244	10
α-helix	247-249	3
α-helix	255-279	25
α-helix	288-314	27
α-helix	318-417	30

Chain E: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	34	1
β-strand	42-52	11	9
β-strand	56-57	2	9
β-strand	62-74	13	9
α-helix	76-78	3
β-strand	86-89	4	9
α-helix	91-94	4
β-strand	102-104	3	10
β-strand	107-112	6	9
β-strand	120-125	6	9
β-strand	129-141	13	9
β-strand	153-156	4	10
β-strand	159-162	4	10
β-strand	170-174	5	9
β-strand	182-184	3	9
β-strand	194-209	16	10
β-strand	211-224	14	10
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-245	11
α-helix	247-249	3
α-helix	255-279	25
α-helix	288-313	26
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	361	Homo sapiens	P31644 (AlphaFold model)

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

>8BGI_1 Gamma-aminobutyric acid receptor subunit alpha-5 (chains A, B, C, D, E)
QMPTSSVKDETNDNITIFTRILDGLLDGYDNRLRPGLGERITQVRTDMYVNSFGPVSDTE
MEYTIDIFFAQTWKDERLRFKGPMQRLPLDNRVADQIWTPDTFFHNDKKSFAHGMTTPNK
MLRIWNDGRVLYTMRLTISAECPMDLEDFPMDEQNCPLKFGSYAYPNSEVVYVWTNGSTK
SVVVAEDGSRLNQYHLMGQTVGTENISTSTGEYTIMTAHFHLKRKIGYFVIQTYLPCIMT
VILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFV
FSALIEFATVNYFTKSQPARAAKIDKMSRIVFPILFGTFNLVYWATYLNRGTTETSQVAP
A

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
P9N	Pregnanolone	C21 H34 O2	5
FYP	ethyl 8-fluoro-5-methyl-6-oxo-5,6-dihydro-4H-imidazo[1,5-a][1,4]benzodiazepine-…	C15 H14 F N3 O3	5

Water and common crystallization additives (SO4) are not listed.

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
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
5O8F 3.2 Å, Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25 and…

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