9FFL: Alpha1beta3 GABA(A) receptor

Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived symmetric bound-closed 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, Helicobacter pylori G27
Chains: 6
Atoms: 15,223
Mol. weight: 296.05 kDa
Ligands: POV, ABU, D10, R16
Released: 4 Jun 2025

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

Secondary structure: helices and β-sheets

9FFL contains 63 α-helices and 78 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: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-54	16	8
β-strand	59-71	13	8
α-helix	73-75	3
β-strand	83-86	4	8
α-helix	88-93	6
β-strand	99-101	3	9
β-strand	104	1	8
β-strand	108-109	2	8
β-strand	117-122	6	8
β-strand	126-138	13	8
β-strand	150-159	10	9
β-strand	167-171	5	8
α-helix	175-177	3
β-strand	179-181	3	8
β-strand	186	1	8
β-strand	191-205	15	9
β-strand	208-221	14	9
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	386-416	31

Chain B: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	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	110	1	7
β-strand	114-118	5	5
β-strand	123-135	13	5
β-strand	147-156	10	6
β-strand	164-168	5	5
α-helix	171-173	3
β-strand	175-176	2	5
α-helix	178-180	3
β-strand	188-200	13	6
β-strand	203-215	13	6
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	310-445	29

Chain C: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-47	12	10
β-strand	51	1	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	7
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	7
β-strand	164-168	5	10
α-helix	171-173	3
β-strand	175-176	2	10
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	280-305	26
α-helix	310-445	29

Chain D: 11 helices, 15 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	83-86	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	175-177	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	232-243	12
α-helix	244-246	3
α-helix	252-273	22
α-helix	285-309	25
α-helix	386-417	32

Chain E: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	35	1
β-strand	36-51	16	4
β-strand	56-68	13	4
α-helix	70-72	3
β-strand	81-83	3	4
α-helix	85-89	5
β-strand	96-98	3	3
β-strand	101-106	6	4
β-strand	114-118	5	4
β-strand	123-135	13	4
α-helix	140-142	3
β-strand	147-156	10	3
β-strand	164-168	5	4
α-helix	171-173	3
β-strand	175-176	2	4
β-strand	186-200	15	3
β-strand	203-216	14	3
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	280-305	26
α-helix	310-445	29

Chain F: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	11
β-strand	407-414	8	11
β-strand	421-427	7	12
β-strand	433-440	8	12
β-strand	446-448	3	12
α-helix	450-452	3
β-strand	456-461	6	11
β-strand	466-471	6	11
α-helix	476-478	3
β-strand	480-487	8	12
α-helix	497-499	3
β-strand	500-503	4	12
β-strand	508-509	2	12

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, C, E	protein	395	Homo sapiens	P28472 (AlphaFold model)
Megabody25,Outer membrane protein	F	protein	522	Lama glama, Helicobacter pylori G27	B5Z8H1 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9FFL_1 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, D)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPDYDIPTTENLYFQGTGQPSQDE
LKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFR
QSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTL
LYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSR
LNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWL
NRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATV
NYFTKSQPARAAKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

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

>9FFL_2 Gamma-aminobutyric acid receptor subunit beta-3 (chains B, C, E)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPDYDIPTTENLYFQGTGQSVNDP
GNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQY
WRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLY
GLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQF
SIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDA
SAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIF
FSQPARAAAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 3 (F), FASTA

>9FFL_3 Megabody25,Outer membrane protein (chains F)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSR
LLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGY
AVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLS
IEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGHTFNYPI
MGWFRQAPGKEREFVGAISWSGGSTSYADSVKDRFTISRDNAKNTVYLEMNNLKPEDTAV
YYCAAKGRYSGGLYYPTNYDYWGQGTQVTVSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	2
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
D10	Decane	C10 H22	6
R16	Hexadecane	C16 H34	1

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

Primary citation

Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived symmetric pre-active 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…

Browse structure collections

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