9FAX: Human full-length beta3gamma2 GABA(A) receptor

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state. Determined by electron microscopy at 2.9 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Lama glama
Chains: 10
Atoms: 19,317
Mol. weight: 367.08 kDa
Ligands: PLM, D10, HEX, PGW
Released: 2 Jul 2025

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

Secondary structure: helices and β-sheets

9FAX contains 90 α-helices and 95 β-strands across 10 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: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	28	1
α-helix	35	1
β-strand	36-41	6	10
β-strand	42-43	2	11
β-strand	44-51	8	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	12
β-strand	104-106	3	10
β-strand	114-118	5	10
β-strand	123-135	13	10
β-strand	137	1	12
α-helix	140-142	3
β-strand	147-156	10	12
β-strand	164-168	5	10
α-helix	171-173	3
β-strand	175-176	2	11
β-strand	186-199	14	12
β-strand	204-216	13	12
α-helix	220-221	2
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-240	3
α-helix	247-269	23
α-helix	280-305	26
α-helix	422-446	25

Chain B: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	28	1
α-helix	35	1
β-strand	36-51	16	8
β-strand	56-68	13	8
β-strand	81-83	3	8
α-helix	84	1
α-helix	85-89	5
β-strand	96-98	3	9
β-strand	101-106	6	8
β-strand	114-118	5	8
β-strand	123-135	13	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	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	280-303	24
α-helix	304-308	5
α-helix	422-445	24

Chain C: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	27-33	7
β-strand	51-66	16	15
β-strand	71-83	13	15
α-helix	85-87	3
β-strand	96-97	2	15
α-helix	100-105	6
β-strand	112-113	2	16
β-strand	116-120	5	15
β-strand	125	1	14
β-strand	129-133	5	15
β-strand	138-150	13	15
β-strand	162-170	9	16
β-strand	179-183	5	15
β-strand	189-190	2	15
α-helix	193-195	3
β-strand	201-214	14	16
β-strand	219-231	13	16
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-253	12
α-helix	254-256	3
α-helix	262-281	20
α-helix	282-285	4
α-helix	295-323	29
α-helix	375-379	5
α-helix	399-401	3
α-helix	402-426	25

Chain D: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	35	1
β-strand	36-51	16	13
β-strand	56-68	13	13
α-helix	70-72	3
α-helix	80	1
β-strand	81	1	13
α-helix	85-90	6
β-strand	96-98	3	14
β-strand	101-106	6	13
β-strand	114-118	5	13
β-strand	123-135	13	13
α-helix	140-142	3
β-strand	147-156	10	14
β-strand	164-168	5	13
α-helix	171-174	4
β-strand	175-176	2	13
β-strand	186-199	14	14
β-strand	204-216	13	14
α-helix	217	1
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-241	4
α-helix	247-269	23
α-helix	280-302	23
α-helix	303-308	6
α-helix	422-446	25

Chain E: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
β-strand	51-62	12	1
β-strand	71	1	2
β-strand	74-83	10	1
β-strand	95-98	4	1
α-helix	102-104	3
β-strand	111-113	3	3
β-strand	116	1	4
β-strand	130-134	5	1
β-strand	138-142	5	1
β-strand	145-147	3	1
β-strand	149	1	4
β-strand	150	1	2
α-helix	155-157	3
β-strand	162-171	10	3
β-strand	179-183	5	1
β-strand	190	1	1
α-helix	193-195	3
β-strand	201-212	12	3
β-strand	221-231	11	3
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	295-318	24
α-helix	319-324	6
α-helix	375-378	4
α-helix	397-399	3
α-helix	402-422	21
α-helix	423-427	5

Chain F: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	20
β-strand	405-413	9	20
β-strand	420-426	7	21
β-strand	432-438	7	21
β-strand	446-447	2	21
β-strand	455-460	6	20
β-strand	465-470	6	20
α-helix	475-477	3
β-strand	479-486	8	21
β-strand	499-502	4	21
β-strand	506-508	3	21

Chains G and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	673-698	26

Chain I: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	17-42	26
β-strand	47-48	2	5
β-strand	57-59	3	5
β-strand	64-66	3	5
β-strand	76-78	3	5
β-strand	80	1	6
β-strand	83	1	6
α-helix	84-86	3
α-helix	90-112	23
α-helix	113-117	5
α-helix	121-145	25
α-helix	147-151	5
α-helix	153-158	6
β-strand	164	1	7
β-strand	167	1	7
α-helix	175-199	25

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
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2	C, E	protein	405	Homo sapiens	P18507 (AlphaFold model)
Neuroligin-2	G, H	protein	33	Homo sapiens	Q8NFZ4 (AlphaFold model)
LHFPL tetraspan subfamily member 4 protein	I, L	protein	188	Homo sapiens	Q7Z7J7 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	A, B, D	protein	439	Homo sapiens	P28472 (AlphaFold model)
Megabody25	F	protein	522	Lama glama

Sequence of entity 1 (C, E), FASTA

>9FAX_1 Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2 (chains C, E)
GDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQTWYD
RRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLYTLR
LTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQFSFV
GLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDAVPA
RTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSNR
KPSKDKDKKKKNPAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCCFED
CRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYLG

Sequence of entity 2 (G, H), FASTA

>9FAX_2 Neuroligin-2 (chains G, H)
DSRDYSTELSVTVAVGASLLFLNILAFAALYYK

Sequence of entity 3 (I, L), FASTA

>9FAX_3 LHFPL tetraspan subfamily member 4 protein (chains I, L)
MRNSRAIGVLWAIFTICFAIINVVVFIQPYWVGDSVSTPKPGYFGLFHYCVGSGLAGREL
TCRGSFTDFSTIPSSAFKAAAFFVLLSMVLILGCITCFSLFFFCNTATVYKICAWMQLLA
ALCLVLGCMIFPDGWDAETIRDMCGAKTGKYSLGDCSVRWAYILAIIGILNALILSFLAF
VLGNRQTD

Sequence of entity 4 (A, B, D), FASTA

>9FAX_4 Gamma-aminobutyric acid receptor subunit beta-3 (chains A, B, D)
MSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWR
DKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGL
RITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQFSI
VEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDASA
ARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFG
RGPQRQKKLAEKTAKAKNDRSKSESNRVDAHGNILLTSLEVHNEMNEVSGGIGDTRNSAI
SFDNSGIQYRKQSMPREGHGRFLGDRSLPHKKTHLRRRSSQLKIKIPDLTDVNAIDRWSR
IVFPFTFSLFNLVYWLYYV

Sequence of entity 5 (F), FASTA

>9FAX_5 Megabody25 (chains F)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSR
LLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGY
AVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLS
IEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGHTFNYPI
MGWFRQAPGKEREFVGAISWSGGSTSYADSVKDRFTISRDNAKNTVYLEMNNLKPEDTAV
YYCAAKGRYSGGLYYPTNYDYWGQGTQVTVSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	5
D10	Decane	C10 H22	5
HEX	Hexane	C6 H14	13
PGW	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexade…	C40 H77 O10 P	4
CLR	Cholesterol	C27 H46 O	2
PX2	1,2-dilauroyl-sn-glycero-3-phosphate	C27 H52 O8 P	2
R16	Hexadecane	C16 H34	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state. Kasaragod, V.B., Aricescu, A.R. To be published.

Other PDB entries of the same protein (UniProt P18507 (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
8BHG 2.39 Å, GABA-A receptor a5 heteromer - a5V2 - Bretazenil
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…
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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