8G4O: Gamma-aminobutyric acid receptor subunit alpha-1

Native GABA-A receptor from the mouse brain, alpha1-beta2-gamma2 subtype, in complex with didesethylflurazepam and endogenous GABA. Determined by electron microscopy at 3.06 Å resolution. Released 20 Sept 2023.

Method: Electron microscopy
Resolution: 3.06 Å
Organism: Mus musculus
Chains: 9
Atoms: 17,353
Mol. weight: 380.03 kDa
Ligands: ABU, YNL, NAG
Released: 20 Sept 2023

Explore 8G4O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G4O contains 60 α-helices and 137 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: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	10-21	12
β-strand	38-43	6	1
β-strand	44-53	10	2
β-strand	58-65	8	2
β-strand	66-69	4	1
β-strand	70	1	3
β-strand	82-85	4	4
α-helix	87-90	4
β-strand	98-100	3	5
β-strand	103-107	5	2
β-strand	112	1	6
β-strand	116	1	2
β-strand	118-121	4	4
β-strand	125	1	3
β-strand	126-127	2	4
β-strand	130-137	8	2
β-strand	149-152	4	7
β-strand	156-158	3	5
β-strand	166-170	5	1
β-strand	178-180	3	2
β-strand	185	1	2
β-strand	190-203	14	7
β-strand	208-220	13	7
α-helix	223-225	3
α-helix	226-230	5
α-helix	231-246	16
α-helix	251-275	25
α-helix	285-309	25
α-helix	390-416	27

Chain B: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
α-helix	35	1
β-strand	36-51	16	8
β-strand	56-67	12	8
β-strand	81	1	8
α-helix	85-90	6
β-strand	96-98	3	9
β-strand	101-106	6	8
β-strand	114-115	2	8
β-strand	118	1	8
β-strand	124-134	11	8
β-strand	147-156	10	9
β-strand	164-168	5	8
α-helix	171-173	3
β-strand	175-176	2	8
β-strand	186-199	14	9
β-strand	204-216	13	9
α-helix	218-221	4
α-helix	222-226	5
α-helix	227-241	15
α-helix	247-268	22
α-helix	278-279	2
α-helix	280-307	28
α-helix	459-486	28

Chain C: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
α-helix	30	1
β-strand	38-48	11	10
β-strand	49	1	11
β-strand	52-53	2	12
β-strand	58-59	2	12
β-strand	62-70	9	10
β-strand	83-85	3	10
α-helix	87-91	5
β-strand	98-100	3	13
β-strand	103	1	14
β-strand	108	1	10
β-strand	112	1	9
β-strand	116-120	5	10
β-strand	125-132	8	10
β-strand	136	1	14
β-strand	137	1	12
β-strand	149-153	5	15
β-strand	156-158	3	13
β-strand	166-170	5	10
α-helix	174-176	3
β-strand	178-180	3	10
β-strand	185	1	11
β-strand	190-204	15	15
β-strand	207-220	14	15
α-helix	223-225	3
α-helix	226-230	5
α-helix	231-245	15
α-helix	251-275	25
α-helix	284-309	26
α-helix	389-416	28

Chain D: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	43	1
β-strand	51-57	7	16
β-strand	59-66	8	16
β-strand	71-82	12	16
β-strand	95-98	4	17
α-helix	100-102	3
β-strand	111-113	3	18
β-strand	116-121	6	16
β-strand	129-130	2	16
β-strand	131-134	4	17
β-strand	139	1	17
β-strand	142-150	9	16
β-strand	163-165	3	18
β-strand	169-171	3	18
β-strand	179-188	10	16
α-helix	193-195	3
β-strand	201-214	14	18
β-strand	219-231	13	18
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-256	15
α-helix	262-283	22
α-helix	295-318	24
α-helix	411-431	21

Chain E: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
α-helix	28	1
α-helix	35	1
β-strand	36-41	6	19
β-strand	42-43	2	20
β-strand	44-51	8	21
β-strand	56-61	6	21
β-strand	64-68	5	19
β-strand	81	1	19
α-helix	85-90	6
β-strand	96-98	3	6
β-strand	104-106	3	21
β-strand	110	1	18
β-strand	114-115	2	19
β-strand	118	1	19
β-strand	123-128	6	19
β-strand	130-135	6	21
β-strand	149-156	8	6
β-strand	164-168	5	19
β-strand	175-176	2	20
β-strand	186-194	9	6
β-strand	197-199	3	22
β-strand	204-206	3	22
β-strand	208-216	9	6
α-helix	218-221	4
α-helix	222-226	5
α-helix	227-240	14
α-helix	248-269	22
α-helix	279-307	29
α-helix	460-487	28

Chain H: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	23
β-strand	10-12	3	24
β-strand	18-23	6	23
β-strand	34-39	6	25
β-strand	46-51	6	25
β-strand	57-59	3	25
α-helix	61-63	3
β-strand	64	1	23
β-strand	67-72	6	23
β-strand	77-82	6	23
β-strand	89-95	7	25
β-strand	100A-103	4	25
β-strand	107-108	2	25
β-strand	109-111	3	24

Chain J: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	26
α-helix	7-9	3
β-strand	10-12	3	27
β-strand	18-24	7	26
α-helix	29-31	3
α-helix	33	1
β-strand	34-39	6	27
β-strand	46-52	7	27
β-strand	56-59	4	27
β-strand	67-72	6	26
β-strand	77-82	6	26
β-strand	88-92	5	27
β-strand	95	1	28
β-strand	100A	1	28
β-strand	107-111	5	27

Chain K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-5	2	29
β-strand	10-12	3	30
β-strand	19-25	7	29
β-strand	33-38	6	30
β-strand	45-48	4	30
α-helix	53	1
β-strand	54	1	30
α-helix	55	1
β-strand	62-66	5	29
β-strand	70-75	6	29
β-strand	85-90	6	30
β-strand	96	1	30
β-strand	101-104	4	30

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 alpha-1	A, C	protein	455	Mus musculus	P62812 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-2	B, E	protein	512	Mus musculus	P63137 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	D	protein	474	Mus musculus	P22723 (AlphaFold model)
Heavy Chain of 8E3 Fab	H, J	protein	223	Mus musculus
Light Chain of 8E3 Fab	K, L	protein	213	Mus musculus

Sequence of entity 1 (A, C), FASTA

>8G4O_1 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, C)
MKKSRGLSDYLWAWTLILSTLSGRSYGQPSQDELKDNTTVFTRILDRLLDGYDNRLRPGL
GERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKI
WTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLYTMRLTVRAECPMHLEDFPMDAHACP
LKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMT
THFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISAR
NSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVPEKPKKVKDPL
IKKNNTYAPTATSYTPNLARGDPGLATIAKSATIEPKEVKPETKPPEPKKTFNSVSKIDR
LSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 2 (B, E), FASTA

>8G4O_2 Gamma-aminobutyric acid receptor subunit beta-2 (chains B, E)
MWRVRKRGYFGIWSFPLIIAAVCAQSVNDPSNMSLVKETVDRLLKGYDIRLRPDFGGPPV
AVGMNIDIASIDMVSEVNMDYTLTMYFQQAWRDKRLSYNVIPLNLTLDNRVADQLWVPDT
YFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIES
YGYTTDDIEFYWRGDDNAVTGVTKIELPQFSIVDYKLITKKVVFSTGSYPRLSLSFKLKR
NIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLTMTTINTHLRETLPKIP
YVKAIDMYLMGCFVFVFMALLEYALVNYIFFGRGPQRQKKAAEKAANANNEKMRLDVNKM
FYKDIKQNGTQYRSLWDPTGDLSPTRRTTNYDFSLYTMDPHENILLSTLEIKNEMATSEA
VMGLGDPRSTMLAYDASSIQYRKAGLPRHSFGRNALERHVAQKKSRLRRRASQLKITIPD
LTDVNAIDRWSRIFFPVVFSFFNIVYWLYYVN

Sequence of entity 3 (D), FASTA

>8G4O_3 Gamma-aminobutyric acid receptor subunit gamma-2 (chains D)
MSSPNTWSIGSSVYSPVFSQKMTLWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPKV
PEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQTW
YDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLYT
LRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQFS
FVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDAV
PARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVS
NRKPSKDKDKKKKNPLLRMFSFKAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGKD
CASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYL

Sequence of entity 4 (H, J), FASTA

>8G4O_4 Heavy Chain of 8E3 Fab (chains H, J)
EIQLQQSGPELVKPGTSVKVSCKASGYSFTDYNMYWVKQSHGKSLEWIGYIDPYNADTTY
NREFKGKATLTVDKSSSTAFMHLNSLTSEDSAVYYCARKRNNFYFDYWGQGTPLTVSSAK
TTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKSAALEVLFQ

Sequence of entity 5 (K, L), FASTA

>8G4O_5 Light Chain of 8E3 Fab (chains K, L)
YIVMTQSPKSMSMSLGERVTLSCRASEYVGSYVSWYQQKPEQSPKLLIYGASNRYTGVPD
RFAGSGSATDFTLTITSVQAEDLADYHCGQTYNYPTFGGGTKLEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
YNL	(5M)-1-(2-aminoethyl)-7-chloro-5-(2-fluorophenyl)-1,3-dihydro-2H-1,4-benzodiaze…	C17 H15 Cl F N3 O	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology. Sun, C., Zhu, H., Clark, S. et al. Nature (2023) 622:195-201. DOI 10.1038/s41586-023-06556-w · PubMed

Other PDB entries of the same protein (UniProt P62812 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FOI 2.5 Å, Native GABA-A receptor from the mouse brain, alpha1-beta2-gamma2 subtype, in complex…
8G4X 2.56 Å, Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-beta2-gamma2 subtype, in…
8G5F 2.64 Å, Native GABA-A receptor from the mouse brain, ortho-alpha1-alpha3-beta2-gamma2 subtype,…
8G4N 2.67 Å, Native GABA-A receptor from the mouse brain, alpha1-beta2-gamma2 subtype, in complex…
5OSA 2.75 Å, GLIC-GABAAR alpha1 chimera crystallized at pH4.6
8G5H 2.89 Å, Native GABA-A receptor from the mouse brain, ortho-alpha1-alpha3-beta2-gamma2 subtype,…
8G5G 2.94 Å, Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-beta2-gamma2 subtype, in…
5OSC 3.1 Å, GLIC-GABAAR alpha1 chimera crystallized in complex with pregnenolone sulfate at pH 4.5
5OSB 3.8 Å, GLIC-GABAAR alpha1 chimera crystallized in complex with THDOC at pH4.5

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