9FFV: Alpha1beta3gamma2 GABA(A) receptor

Cryo-EM structure of the alpha1beta3gamma2 GABA(A) receptor in complex with Nb38 in the long-lived symmetric resting state. Determined by electron microscopy at 2.8 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 15,371
Mol. weight: 249.91 kDa
Ligands: D10
Released: 4 Jun 2025

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

Secondary structure: helices and β-sheets

9FFV contains 66 α-helices and 75 β-strands across 6 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, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	38	1
β-strand	39-54	16	1
β-strand	59-71	13	1
α-helix	73-75	3
β-strand	83-85	3	1
α-helix	88-91	4
β-strand	99-101	3	2
β-strand	104	1	1
β-strand	108-109	2	1
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	191-204	14	2
β-strand	209-221	13	2
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	244-246	3
α-helix	252-276	25
α-helix	285-310	26
α-helix	315-414	29

Chain B: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	35	1
β-strand	36-51	16	3
β-strand	56-68	13	3
α-helix	70-72	3
β-strand	81-83	3	3
α-helix	85-90	6
β-strand	96-98	3	4
β-strand	101-106	6	3
β-strand	114-118	5	3
β-strand	123-135	13	3
β-strand	147-156	10	4
β-strand	164-168	5	3
α-helix	171-173	3
β-strand	175-176	2	3
α-helix	178-180	3
β-strand	186-199	14	4
β-strand	204-216	13	4
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-235	9
α-helix	238-241	4
α-helix	247-271	25
α-helix	280-305	26
α-helix	310-445	29

Chain C: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	50	1
β-strand	51-66	16	5
β-strand	71-83	13	5
α-helix	85-87	3
β-strand	95-99	5	5
α-helix	100-105	6
β-strand	111-113	3	6
β-strand	116-121	6	5
β-strand	129-134	6	5
β-strand	138-150	13	5
β-strand	162-171	10	6
β-strand	179-190	12	5
α-helix	193-195	3
β-strand	201-214	14	6
β-strand	219-231	13	6
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-251	10
α-helix	252-256	5
α-helix	262-281	20
α-helix	293-294	2
α-helix	295-323	29
α-helix	325-423	28
α-helix	424-428	5

Chain D: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
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	88-91	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
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	191-204	14	8
β-strand	209-221	13	8
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	315-417	32

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	9
β-strand	56-68	13	9
α-helix	70-72	3
β-strand	81-83	3	9
α-helix	85-90	6
β-strand	96-98	3	10
β-strand	101-106	6	9
β-strand	110	1	2
β-strand	114-118	5	9
β-strand	123-135	13	9
β-strand	147-156	10	10
β-strand	164-168	5	9
α-helix	171-173	3
β-strand	175-176	2	9
α-helix	178-180	3
β-strand	186-200	15	10
β-strand	203-216	14	10
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-235	9
α-helix	236-241	6
α-helix	247-271	25
α-helix	280-305	26
α-helix	310-446	30

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	11-13	3	2
β-strand	19-26	8	11
β-strand	34-40	7	2
β-strand	46-52	7	2
β-strand	58-60	3	2
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	108-110	3
β-strand	111-114	4	2
β-strand	118-122	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit alpha-1	A, D	protein	411	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	B, E	protein	395	Homo sapiens	P28472 (AlphaFold model)
Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2	C	protein	373	Homo sapiens	P18507 (AlphaFold model)
Nanobody38	F	protein	133	Lama glama

Sequence of entity 1 (A, D), FASTA

>9FFV_1 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, D)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPDYDIPTTENLYFQGTGQPSQDE
LKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFR
QSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTL
LYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSR
LNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWL
NRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATV
NYFTKSQPARAAKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 2 (B, E), FASTA

>9FFV_2 Gamma-aminobutyric acid receptor subunit beta-3 (chains B, E)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPDYDIPTTENLYFQGTGQSVNDP
GNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQY
WRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLY
GLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQF
SIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDA
SAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIF
FSQPARAAAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 3 (C), FASTA

>9FFV_3 Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2 (chains C)
TGQKSDDDYEDYTSNKTWVLTPKVPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMY
VNSIGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKK
ADAHWITTPNRMLRIWNDGRVLYTLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREE
IVYQWKRSSVEVGDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTI
QTYIPCTLIVVLSWVSFWINKDAVPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDL
FVSVCFIFVFSALVEYGTLHYFVSSQPARAAKMDSYARIFFPTAFCLFNLVYWVSYLYLG
TGGTTETSQVAPA

Sequence of entity 4 (F), FASTA

>9FFV_4 Nanobody38 (chains F)
QVQLQESGGGLVQAGGSLRVSCAASGRTFTTYIMAWFRQAPGKEREFLAAMDQGRIQYYG
DSVRGRFTISRDYAKNSVDLQLDGLRPEDTAVYYCAAGAGFWGLRTASSYHYWGQGTQVT
VSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
D10	Decane	C10 H22	5

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

Primary citation

Cryo-EM structure of the alpha1beta3gamma2 GABA(A) receptor in complex with Nb38 in the long-lived symmetric resting 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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