8VQY: Human GABAA receptor alpha1-beta2-gamma2 subtype

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus methaqualone. Determined by electron microscopy at 2.82 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 2.82 Å
Organisms: Homo sapiens, Mus musculus
Chains: 9
Atoms: 17,804
Mol. weight: 371.2 kDa
Ligands: ABU, Q3G, PTY, A1ADG
Released: 26 Jun 2024

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

Secondary structure: helices and β-sheets

8VQY contains 67 α-helices and 112 β-strands across 9 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: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	35	1
β-strand	36-47	12	1
β-strand	51	1	1
β-strand	56-68	13	1
α-helix	70-72	3
β-strand	81-83	3	1
α-helix	85-89	5
β-strand	96-98	3	2
β-strand	101-106	6	1
β-strand	114-118	5	1
β-strand	123-135	13	1
β-strand	147-156	10	2
β-strand	164-168	5	1
β-strand	175-176	2	1
β-strand	186-200	15	2
β-strand	203-216	14	2
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-241	4
α-helix	247-271	25
α-helix	278-279	2
α-helix	280-306	27
α-helix	310-339	30

Chain B: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
β-strand	39-49	11	3
β-strand	53-54	2	3
β-strand	59-71	13	3
α-helix	73-75	3
β-strand	83-86	4	3
α-helix	91-93	3
β-strand	99-101	3	4
β-strand	104-109	6	3
β-strand	113	1	2
β-strand	117-122	6	3
β-strand	126-138	13	3
β-strand	150-159	10	4
β-strand	167-171	5	3
α-helix	175-177	3
β-strand	179-181	3	3
β-strand	191-204	14	4
β-strand	209-221	13	4
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	244-246	3
α-helix	252-274	23
α-helix	285-310	26
α-helix	315-345	31

Chain C: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	35	1
β-strand	36-47	12	5
β-strand	51	1	5
β-strand	56-68	13	5
α-helix	70-72	3
β-strand	82-83	2	5
α-helix	85-90	6
β-strand	96-98	3	6
β-strand	101-106	6	5
β-strand	114-118	5	5
β-strand	123-135	13	5
β-strand	147-156	10	6
β-strand	164-168	5	5
β-strand	175-176	2	5
β-strand	186-200	15	6
β-strand	203-216	14	6
α-helix	217	1
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-238	12
α-helix	239-241	3
α-helix	247-269	23
α-helix	278-279	2
α-helix	280-304	25
α-helix	310-338	29

Chain D: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
β-strand	39-54	16	7
β-strand	59-71	13	7
α-helix	73-75	3
β-strand	83-86	4	7
α-helix	90-93	4
β-strand	99-101	3	8
β-strand	104	1	7
β-strand	108-109	2	7
β-strand	117-122	6	7
β-strand	126-138	13	7
β-strand	150-159	10	8
β-strand	167-171	5	7
α-helix	175-177	3
β-strand	179-181	3	7
β-strand	186	1	7
β-strand	191-205	15	8
β-strand	208-221	14	8
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	244-246	3
α-helix	252-275	24
α-helix	285-310	26
α-helix	315-345	31

Chain E: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	50	1
β-strand	51-66	16	9
β-strand	71-83	13	9
β-strand	95-98	4	9
α-helix	100-105	6
β-strand	111-113	3	10
β-strand	116-121	6	9
β-strand	125	1	8
β-strand	129-134	6	9
β-strand	138-150	13	9
β-strand	162-171	10	10
β-strand	179-190	12	9
β-strand	201-214	14	10
β-strand	219-231	13	10
α-helix	235-236	2
α-helix	237-241	5
α-helix	242-253	12
α-helix	254-256	3
α-helix	263-265	3
α-helix	267-286	20
α-helix	295-323	29
α-helix	325-355	31

Chain I: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-48	4	12
β-strand	54	1	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
β-strand	96-97	2	12
β-strand	102-104	3	12

Chain J: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	46-51	6	14
β-strand	58-60	3	14
β-strand	65	1	13
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-98	7	14
β-strand	107-108	2	14
β-strand	112-116	5	14

Chain K: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	45-52	8	19
β-strand	57-60	4	19
α-helix	62-64	3
β-strand	68-73	6	17
β-strand	78-83	6	17
β-strand	93-99	7	19
β-strand	105-108	4	19
β-strand	112-113	2	19
β-strand	114-116	3	18

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit beta-2	A, C	protein	364	Homo sapiens	P47870 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-1	B, D	protein	358	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	E	protein	417	Homo sapiens	P18507 (AlphaFold model)
Kappa FAB light chain	I, L	protein	213	Mus musculus
IGG2B FAB heavy chain	J, K	protein	454	Mus musculus

Sequence of entity 1 (A, C), FASTA

>8VQY_1 Gamma-aminobutyric acid receptor subunit beta-2 (chains A, C)
QSVNDPSNMSLVKETVDRLLKGYDIRLRPDFGGPPVAVGMNIDIASIDMVSEVNMDYTLT
MYFQQAWRDKRLSYNVIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHP
DGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGDDNAVTGVTK
IELPQFSIVDYKLITKKVVFSTGSYPRLSLSFKLKRNIGYFILQTYMPSILITILSWVSF
WINYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFMALLEYA
LVNYIFFSQPARAAAIDRWSRIFFPVVFSFFNIVYWLYYVNVDGSGATNFSLLKQAGDVE
ENPG

Sequence of entity 2 (B, D), FASTA

>8VQY_2 Gamma-aminobutyric acid receptor subunit alpha-1 (chains B, D)
QPSLQDELKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEY
TIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLR
ITEDGTLLYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVV
VAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVIL
SQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSA
LIEFATVNYFTKSQPARAAKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 3 (E), FASTA

>8VQY_3 Gamma-aminobutyric acid receptor subunit gamma-2 (chains E)
WSHPQFEKGGGSGGGSGGSSAWSHPQFEKLEVLFQGPQKSDDDYEDYASNKTWVLTPKVP
EGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQTWY
DRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLYTL
RLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQFSF
VGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDAVP
ARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSS
QPARAAKMDSYARIFFPTAFCLFNLVYWVSYLYLSRGSGATNFSLLKQAGDVEENPG

Sequence of entity 4 (I, L), FASTA

>8VQY_4 Kappa FAB light chain (chains I, L)
NIVMTQSPKSMSMSVGERVTLSCKASEYVGTYVSWYQQKPEQSPKLLIYGASNRYTGVPD
RFTGSGSATDFTLTIGSVQAEDLADYHCGQSYSYPTFGAGTKLELKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (J, K), FASTA

>8VQY_5 IGG2B FAB heavy chain (chains J, K)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMYWVKQRPEQGLEWIGRIDPANGDTKY
DPKFQGKATITTDTFSNTAYLQLSSLTSEDTAVYYCARKGLRWAMDYWGQGTSVTVSTAK
TTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPN
LEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHR
EDYNSTIRVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPP
PAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMK
TSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK

Ligands and cofactors

ID	Name	Formula	Copies
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
Q3G	O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl…	C40 H78 N O10 P	2
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	4
A1ADG	2-methyl-3-(2-methylphenyl)quinazolin-4(3H)-one	C16 H14 N2 O	3

Primary citation

Structural insights into GABA A receptor potentiation by Quaalude. Chojnacka, W., Teng, J., Kim, J.J. et al. Nat Commun (2024) 15:5244-5244. DOI 10.1038/s41467-024-49471-y · PubMed

Other PDB entries of the same protein (UniProt P47870 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6X3T 2.55 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus propofol
8VRN 2.57 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus PPTQ
8SGO 2.65 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus pregnenolone…
8SID 2.71 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus…
6X40 2.86 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus picrotoxin
8DD2 2.9 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus Zolpidem
8DD3 2.9 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus DMCM
9CRS 2.9 Å, Native human GABAA receptor of beta2-alpha1-beta2-alpha1-gamma2 assembly
6X3X 2.92 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus diazepam
9DRX 2.95 Å, Human GABAA receptor of beta2-alpha1-beta2-alpha1-gamma2 subtype in complex with GABA…
8SI9 2.98 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus…
7T0W 3.0 Å, Complex of GABA-A synaptic receptor with autoimmune antibody Fab115

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