9FG9: Full-length alpha1beta3gamma2 GABA(A) receptor

Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Etomidate in the long-lived symmetric desensitised state. Determined by electron microscopy at 2.7 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 5
Atoms: 15,031
Mol. weight: 282.67 kDa
Ligands: LBN, V8D, PIO, ABU
Released: 4 Jun 2025

Explore 9FG9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FG9 contains 67 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: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
β-strand	39-54	16	1
β-strand	59-71	13	1
α-helix	73-75	3
β-strand	83-86	4	1
α-helix	88-93	6
β-strand	99-101	3	2
β-strand	104	1	1
β-strand	108-109	2	1
β-strand	113	1	3
β-strand	117-122	6	1
β-strand	126-138	13	1
β-strand	150-159	10	2
β-strand	167-171	5	1
α-helix	175-178	4
β-strand	179-181	3	1
β-strand	186	1	1
β-strand	191-205	15	2
β-strand	208-221	14	2
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-241	10
α-helix	243-246	4
α-helix	252-272	21
α-helix	285-309	25
α-helix	387-390	4
α-helix	391-415	25

Chain B: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	4
β-strand	56-68	13	4
α-helix	70-72	3
β-strand	82-83	2	4
α-helix	85-90	6
β-strand	96-98	3	3
β-strand	101-106	6	4
β-strand	110	1	5
β-strand	114-118	5	4
β-strand	123-135	13	4
β-strand	147-156	10	3
β-strand	164-168	5	4
α-helix	171-174	4
β-strand	175-176	2	4
α-helix	178-180	3
β-strand	186-200	15	3
β-strand	203-216	14	3
α-helix	217	1
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-235	9
α-helix	236-240	5
α-helix	247-269	23
α-helix	278-279	2
α-helix	280-303	24
α-helix	304-308	5
α-helix	420-446	27

Chain C: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	50	1
β-strand	51-66	16	6
β-strand	71-83	13	6
α-helix	85-87	3
β-strand	95-98	4	6
α-helix	100-102	3
β-strand	111-113	3	5
β-strand	116-121	6	6
β-strand	129-134	6	6
β-strand	138-150	13	6
β-strand	162-171	10	5
β-strand	179-190	12	6
α-helix	193-195	3
β-strand	201-215	15	5
β-strand	218-231	14	5
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-252	11
α-helix	253-256	4
α-helix	262-283	22
α-helix	295-321	27
α-helix	410-434	25

Chain D: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
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	113	1	9
β-strand	117-122	6	7
β-strand	126-138	13	7
α-helix	143-145	3
β-strand	150-159	10	8
β-strand	167-171	5	7
α-helix	175-178	4
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	232-241	10
α-helix	242-246	5
α-helix	252-273	22
α-helix	285-309	25
α-helix	322-323	2
α-helix	387-390	4
α-helix	391-417	27

Chain E: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	10
β-strand	56-68	13	10
α-helix	70-72	3
β-strand	81-83	3	10
α-helix	85-90	6
β-strand	96-98	3	9
β-strand	101-106	6	10
β-strand	110	1	2
β-strand	114-118	5	10
β-strand	123-135	13	10
β-strand	147-156	10	9
β-strand	164-168	5	10
α-helix	171-173	3
β-strand	175-176	2	10
β-strand	186-200	15	9
β-strand	203-216	14	9
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-241	5
α-helix	247-270	24
α-helix	280-303	24
α-helix	304-308	5
α-helix	420-445	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit alpha-1	A, D	protein	464	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	B, E	protein	473	Homo sapiens	P28472 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	C	protein	495	Homo sapiens	P18507 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9FG9_1 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, D)
MKKSPGLSDYLWAWTLFLSTLTGRSYGDYKDDDDKQPSLQDELKDNTTVFTRILDRLLDG
YDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLR
LNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLYTMRLTVRAECPMHLED
FPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQS
STGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLT
MTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVPE
KPKKVKDPLIKKNNTYAPTATSYTPNLARGDPGLATIAKSATIEPKEVKPETKPPEPKKT
FNSVSKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 2 (B, E), FASTA

>9FG9_2 Gamma-aminobutyric acid receptor subunit beta-3 (chains B, E)
MCSGLLELLLPIWLSWTLGTRGSEPRSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP
VCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPD
TYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIE
SYGYTTDDIEFYWRGGDKAVTGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLK
RNIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLTMTTINTHLRETLPKI
PYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAEKTAKAKNDRSKSESNR
VDAHGNILLTSLEVHNEMNEVSGGIGDTRNSAISFDNSGIQYRKQSMPREGHGRFLGDRS
LPHKKTHLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 3 (C), FASTA

>9FG9_3 Gamma-aminobutyric acid receptor subunit gamma-2 (chains C)
MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK
VPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQT
WYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLY
TLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQF
SFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDA
VPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFV
SNRKPSKDKDKKKKNPLLRMFSFKAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGK
DCASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYLGGSGG
SGGSGKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
LBN	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine	C42 H82 N O8 P	2
V8D	Etomidate	C14 H16 N2 O2	2
PIO	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-d…	C25 H49 O19 P3	2
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
R16	Hexadecane	C16 H34	2
D10	Decane	C10 H22	5

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

Primary citation

Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Etomidate in the long-lived symmetric desensitised state. Mihaylov, D.B., Malinauskas, T., Aricescu, A.R. To be published.

Other PDB entries of the same protein (UniProt P14867 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RGD 2.0 Å, CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
9EQG 2.4 Å, CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA…
9FAS 2.5 Å, CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with…
9FFU 2.5 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…
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
8PET 2.6 Å, Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba…
9FAJ 2.6 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with…
9FAK 2.6 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with…
9FGG 2.6 Å, Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in Saposin A…
8SGO 2.65 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus pregnenolone…
7QNE 2.7 Å, Cryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex…

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