8PET: Full-length human alpha1beta3 GABA(A) receptor

Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1. Determined by electron microscopy at 2.6 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 15,451
Mol. weight: 300.54 kDa
Ligands: R16, PIO, D10, ZN
Released: 2 Jul 2025

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

Secondary structure: helices and β-sheets

8PET contains 70 α-helices and 79 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	13-22	10
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	175-177	3
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	232-242	11
α-helix	243-246	4
α-helix	252-276	25
α-helix	285-308	24
α-helix	387-390	4
α-helix	391-415	25

Chain B: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	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	110	1	5
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	188-199	12	4
β-strand	204-215	12	4
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	445-471	27

Chain C: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-54	16	9
β-strand	59-71	13	9
α-helix	73-75	3
β-strand	83-86	4	9
α-helix	87	1
α-helix	88-91	4
β-strand	99-101	3	5
β-strand	104-109	6	9
β-strand	113	1	7
β-strand	117-122	6	9
β-strand	126-138	13	9
α-helix	143-145	3
β-strand	150-159	10	5
β-strand	167-171	5	9
α-helix	175-178	4
β-strand	179-181	3	9
β-strand	186	1	9
β-strand	191-204	14	5
β-strand	209-221	13	5
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	285-309	25
α-helix	387-390	4
α-helix	391-415	25

Chain D: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	35	1
β-strand	36-51	16	6
β-strand	56-68	13	6
α-helix	70-72	3
β-strand	82-83	2	6
α-helix	85-90	6
β-strand	96-98	3	7
β-strand	101-106	6	6
β-strand	110	1	8
β-strand	114-118	5	6
β-strand	123-135	13	6
β-strand	147-156	10	7
β-strand	164-168	5	6
α-helix	171-173	3
β-strand	175-176	2	6
α-helix	178-180	3
β-strand	186-200	15	7
β-strand	203-216	14	7
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-241	5
α-helix	247-271	25
α-helix	280-307	28
α-helix	445-471	27

Chain E: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	35	1
β-strand	36-51	16	10
β-strand	56-68	13	10
α-helix	70-72	3
β-strand	82-83	2	10
α-helix	85-90	6
β-strand	96-98	3	8
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	8
β-strand	164-168	5	10
α-helix	171-173	3
β-strand	175-176	2	10
β-strand	186-200	15	8
β-strand	203-216	14	8
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-241	5
α-helix	247-266	20
α-helix	269-271	3
α-helix	280-303	24
α-helix	304-308	5
α-helix	445-471	27

Chain F: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	11
β-strand	11-12	2	12
β-strand	17-26	10	11
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	68-73	6	11
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	92-99	8	13
α-helix	109-111	3
β-strand	112-115	4	13
α-helix	118	1
β-strand	119-121	3	13
β-strand	122-123	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit alpha-1	A, C	protein	484	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	B, D, E	protein	490	Homo sapiens	P28472 (AlphaFold model)
Nanobody Nb25	F	protein	135	Lama glama

Sequence of entity 1 (A, C), FASTA

>8PET_1 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, C)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGWSHPQFEKGGGSGGGSGGSAWSHPQFEKG
GSTGDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVF
FRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDG
TLLYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDG
SRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSF
WLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFA
TVNYFTKRGYAWDGKSVVPEKPKKVKDPLIKKNNTYAPTATSYTPNLARGDPGLATIAKS
ATIEPKEVKPETKPPEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAP
TPHQ

Sequence of entity 2 (B, D, E), FASTA

>8PET_2 Gamma-aminobutyric acid receptor subunit beta-3 (chains B, D, E)
MGILPSPGMPALLSLVSLLSVLLMGCVAEYPYDVPDYATGQSVNDPGNMSFVKETVDKLL
KGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLN
LTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDL
RRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQFSIVEHRLVSRNVVF
ATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLT
MTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAEK
TAKAKNDRSKSESNRVDAHGNILLTSLEVHNEMNEVSGGIGDTRNSAISFDNSGIQYRKQ
SMPREGHGRFLGDRSLPHKKGTTHLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLF
NLVYWLYYVN

Sequence of entity 3 (F), FASTA

>8PET_3 Nanobody Nb25 (chains F)
QVQLQESGGGLVQAGGSLRLSCAASGHTFNYPIMGWFRQAPGKEREFVGAISWSGGSTSY
ADSVKDRFTISRDNAKNTVYLEMNNLKPEDTAVYYCAAKGRYSGGLYYPTNYDYWGQGTQ
VTVSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
R16	Hexadecane	C16 H34	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
D10	Decane	C10 H22	12
ZN	Zinc ion	Zn	1

Primary citation

Subunit abundance shapes GABAA receptor stoichiometry. Sente, A., Malinauskas, T., Naydenova, K. et al. 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
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…
9FG7 2.7 Å, Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in complex with…

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