8BHG: GABA-A receptor a5 heteromer - a5V2 - Bretazenil

GABA-A receptor a5 heteromer - a5V2 - Bretazenil. Determined by X-ray diffraction at 2.39 Å resolution. Released 15 Nov 2023.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,961
Mol. weight: 210.36 kDa
Ligands: DMU, NAG, QMU
Released: 15 Nov 2023

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

Secondary structure: helices and β-sheets

8BHG contains 50 α-helices and 67 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: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	15-26	12
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	91-93	3
β-strand	102-104	3	2
β-strand	107-112	6	1
β-strand	116	1	3
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	194-208	15	2
β-strand	211-224	14	2
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-245	11
α-helix	246-249	4
α-helix	255-278	24
α-helix	288-313	26
α-helix	318-455	31

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-35	12
α-helix	50	1
β-strand	51-66	16	4
β-strand	71-83	13	4
α-helix	85-87	3
β-strand	95-98	4	4
α-helix	100-105	6
β-strand	111-113	3	3
β-strand	116-121	6	4
β-strand	129-134	6	4
β-strand	138-150	13	4
β-strand	162-165	4	3
β-strand	169-171	3	3
β-strand	179-190	12	4
β-strand	201-214	14	3
β-strand	219-231	13	3
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-253	12
α-helix	254-256	3
α-helix	262-285	24
α-helix	295-321	27
α-helix	325-462	31

Chain C: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	15-26	12
β-strand	42-57	16	5
β-strand	62-74	13	5
α-helix	76-78	3
β-strand	86-89	4	5
β-strand	102-104	3	6
β-strand	107-112	6	5
β-strand	116	1	7
β-strand	120-125	6	5
β-strand	129-141	13	5
β-strand	153-156	4	6
β-strand	160-162	3	6
β-strand	170-174	5	5
β-strand	182-184	3	5
β-strand	194-208	15	6
β-strand	211-224	14	6
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-245	11
α-helix	246-249	4
α-helix	255-278	24
α-helix	288-313	26
α-helix	318-453	29

Chain D: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
β-strand	42-57	16	8
β-strand	62-74	13	8
α-helix	76-78	3
β-strand	86-89	4	8
α-helix	91-94	4
β-strand	102-104	3	7
β-strand	107-112	6	8
β-strand	116	1	9
β-strand	120-125	6	8
β-strand	129-141	13	8
β-strand	153-156	4	7
β-strand	159-162	4	7
β-strand	170-174	5	8
β-strand	182-184	3	8
β-strand	194-208	15	7
β-strand	211-224	14	7
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-245	11
α-helix	246-249	4
α-helix	255-278	24
α-helix	288-313	26
α-helix	318-454	30

Chain E: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	15-26	12
β-strand	42-57	16	10
β-strand	62-74	13	10
α-helix	76-78	3
β-strand	88-89	2	10
α-helix	92-96	5
β-strand	102-104	3	9
β-strand	107-112	6	10
β-strand	120-124	5	10
β-strand	129-141	13	10
β-strand	153-156	4	9
β-strand	160-162	3	9
β-strand	170-174	5	10
β-strand	182-184	3	10
β-strand	194-208	15	9
β-strand	211-224	14	9
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-245	11
α-helix	246-249	4
α-helix	255-278	24
α-helix	288-313	26
α-helix	318-454	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit alpha-5	A, C, D, E	protein	350	Homo sapiens	P31644 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	B	protein	379	Homo sapiens	P18507 (AlphaFold model)

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

>8BHG_1 Gamma-aminobutyric acid receptor subunit alpha-5 (chains A, C, D, E)
QMPTSSVKDETNDNITIFTRILDGLLDGYDNRLRPGLGERITQVRTDMYVNSFGPVSDTE
MEYTIDIFFAQTWKDERLRFKGPMQRLPLDNRVADQIWTPDTFFHNDKKSFAHGMTTPNK
MLRIWNDGRVLYTMRLTISAECPMDLEDFPMDEQNCPLKFGSYAYPNSEVVYVWTNGSTK
SVVVAEDGSRLNQYHLMGQTVGTENISTSTGEYTIMTAHFHLKRKIGYFVIQTYLPCIMT
VILSQVSFWLNRESVAARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFV
FSALLEFAFVNYITKSQPARAAKIDKMSRIVFPILFGTFNLVYWATYLNR

Sequence of entity 2 (B), FASTA

>8BHG_2 Gamma-aminobutyric acid receptor subunit gamma-2 (chains B)
QKSDDDYEDYTSNKTWVLTPKVPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVN
SIGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKAD
AHWITTPNRMLRIWNDGRVLYTLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIV
YQWKRSSVEVGDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRIGYFVIQT
YLPCIMTVILSQVSFWLNRESVAARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFI
AVCYAFVFSALIEFATVNYFTKSQPARAAKIDRLSRIAFPLLFGIFNLVYWATYLNREPQ
LKAPTPHQGTTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
DMU	Decyl-beta-D-maltopyranoside	C22 H42 O11	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
QMU	Bretazenil	C19 H20 Br N3 O3	5

Water and common crystallization additives (NO3) 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:

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

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