9FAT: Human full-length alpha1beta3gamma2 GABA(A)R

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, Megabody38 and pregnenolone sulfate. Determined by electron microscopy at 3.6 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Lama glama
Chains: 8
Atoms: 17,913
Mol. weight: 338.96 kDa
Ligands: PIO, PGW, D10, R16
Released: 2 Jul 2025

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

Secondary structure: helices and β-sheets

9FAT contains 82 α-helices and 104 β-strands across 8 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, 19 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-44	6	1
β-strand	46-54	9	2
β-strand	59-64	6	2
β-strand	67-70	4	1
β-strand	71	1	3
α-helix	73-75	3
β-strand	83-86	4	1
α-helix	88-93	6
β-strand	100-101	2	4
β-strand	104	1	2
β-strand	108-109	2	2
β-strand	118-122	5	1
β-strand	126	1	3
β-strand	129-130	2	1
β-strand	133-138	6	2
β-strand	150-158	9	4
β-strand	167-171	5	1
α-helix	175-178	4
β-strand	180-181	2	2
β-strand	186	1	2
β-strand	191-204	14	4
β-strand	209-221	13	4
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-242	11
α-helix	243-245	3
α-helix	252-272	21
α-helix	285-310	26
α-helix	387-390	4
α-helix	391-416	26

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-41	6	5
β-strand	42-43	2	6
β-strand	44-51	8	7
β-strand	56-61	6	7
β-strand	64-68	5	5
α-helix	70-72	3
β-strand	81-83	3	5
α-helix	85-90	6
β-strand	96-98	3	8
β-strand	101-106	6	7
β-strand	114-118	5	5
β-strand	123-128	6	5
β-strand	130-135	6	7
α-helix	140-142	3
β-strand	147-156	10	8
β-strand	164-168	5	5
β-strand	175-176	2	6
β-strand	186-200	15	8
β-strand	203-216	14	8
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	280-303	24
α-helix	304-308	5
α-helix	310-316	7
α-helix	414-416	3
α-helix	420-446	27

Chain C: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	43	1
β-strand	51-66	16	9
β-strand	71-83	13	9
α-helix	85-87	3
β-strand	95-98	4	9
α-helix	100-102	3
β-strand	111-113	3	10
β-strand	116-121	6	9
β-strand	129-134	6	9
β-strand	138-150	13	9
β-strand	162-171	10	10
β-strand	179-182	4	9
β-strand	188-190	3	9
α-helix	193-195	3
β-strand	201-215	15	10
β-strand	218-231	14	10
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-253	12
α-helix	254-256	3
α-helix	262-283	22
α-helix	284-286	3
α-helix	295-318	24
α-helix	319-323	5
α-helix	375-378	4
α-helix	402-423	22
α-helix	424-428	5

Chain D: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
β-strand	34	1	11
β-strand	37	1	11
β-strand	39-44	6	12
β-strand	45-54	10	13
β-strand	59-64	6	13
β-strand	67-71	5	12
α-helix	73-75	3
β-strand	83-86	4	12
α-helix	89-93	5
β-strand	100-101	2	14
β-strand	108-109	2	13
β-strand	117-122	6	12
β-strand	126-131	6	12
β-strand	133-138	6	13
β-strand	150-158	9	14
β-strand	167-171	5	12
α-helix	175-178	4
β-strand	179-181	3	13
β-strand	186	1	13
β-strand	191-199	9	14
β-strand	202-203	2	15
β-strand	210-211	2	15
β-strand	212-221	10	14
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-242	11
α-helix	243-246	4
α-helix	252-271	20
α-helix	274-276	3
α-helix	285-310	26
α-helix	387-390	4
α-helix	391-417	27

Chain E: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-40	5	16
β-strand	43-47	5	16
β-strand	51	1	16
β-strand	56-68	13	16
β-strand	81-83	3	16
α-helix	85-90	6
β-strand	96-97	2	17
β-strand	101-106	6	16
β-strand	114-118	5	16
β-strand	123-135	13	16
β-strand	147-154	8	18
β-strand	155-156	2	17
β-strand	164-168	5	16
α-helix	171-173	3
β-strand	176	1	16
β-strand	186-199	14	18
β-strand	204-216	13	18
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	280-303	24
α-helix	304-308	5
α-helix	310-316	7
α-helix	420-446	27

Chain G: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	424-431	8	19
β-strand	440-446	7	4
β-strand	450-457	8	4
β-strand	462-465	4	4
α-helix	467-469	3
β-strand	470	1	19
β-strand	473-478	6	19
β-strand	483-488	6	19
α-helix	493-495	3
β-strand	497-503	7	4
α-helix	513-515	3
β-strand	518-519	2	4
β-strand	523-525	3	4
β-strand	526-527	2	20

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	674-698	25

Chain L: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-42	28
β-strand	47-48	2	21
β-strand	57-59	3	21
β-strand	64-67	4	21
β-strand	75-78	4	21
β-strand	80	1	22
β-strand	83	1	22
α-helix	84-86	3
α-helix	90-112	23
α-helix	113-117	5
α-helix	121-145	25
α-helix	146-151	6
α-helix	153-159	7
β-strand	164	1	23
β-strand	167	1	23
β-strand	172-173	2	21
α-helix	175-202	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit alpha-1	A, D	protein	413	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	B, E	protein	441	Homo sapiens	P28472 (AlphaFold model)
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2	C	protein	405	Homo sapiens	P18507 (AlphaFold model)
Megabody38	G	protein	539	Lama glama
Neuroligin-2	H	protein	33	Homo sapiens	Q8NFZ4 (AlphaFold model)
LHFPL tetraspan subfamily member 4 protein	L	protein	190	Homo sapiens	Q7Z7J7

Sequence of entity 1 (A, D), FASTA

>9FAT_1 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, D)
DNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQS
WKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLY
TMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLN
QYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNR
ESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNY
FTKRGYAWDGKSVVPEKPKKVKDPLIKKNNTYAPTATSYTPNLARGDPGLATIAKSATIE
PKEVKPETKPPEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWATYLNREPQL

Sequence of entity 2 (B, E), FASTA

>9FAT_2 Gamma-aminobutyric acid receptor subunit beta-3 (chains B, E)
GNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQY
WRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLY
GLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQF
SIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDA
SAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIF
FGRGPQRQKKLAEKTAKAKNDRSKSESNRVDAHGNILLTSLEVHNEMNEVSGGIGDTRNS
AISFDNSGIQYRKQSMPREGHGRFLGDRSLPHKKTHLRRRSSQLKIKIPDLTDVNAIDRW
SRIVFPFTFSLFNLVYWLYYV

Sequence of entity 3 (C), FASTA

>9FAT_3 Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2 (chains C)
GDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQTWYD
RRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLYTLR
LTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQFSFV
GLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDAVPA
RTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSNR
KPSKDKDKKKKNPAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCCFED
CRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYLG

Sequence of entity 4 (G), FASTA

>9FAT_4 Megabody38 (chains G)
QVQLQESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRASGG
GSGGGGSGKLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAY
QATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNG
THSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSK
YGSLRVSCAASGRTFTTYIMAWFRQAPGKEREFLAAMDQGRIQYYGDSVRGRFTISRDYA
KNSVDLQLDGLRPEDTAVYYCAAGAGFWGLRTASSYHYWGQGTQVTVSSHHHHHHEPEA

Sequence of entity 5 (H), FASTA

>9FAT_5 Neuroligin-2 (chains H)
DSRDYSTELSVTVAVGASLLFLNILAFAALYYK

Sequence of entity 6 (L), FASTA

>9FAT_6 LHFPL tetraspan subfamily member 4 protein (chains L)
HYMRNSRAIGVLWAIFTICFAIINVVVFIQPYWVGDSVSTPKPGYFGLFHYCVGSGLAGR
ELTCRGSFTDFSTIPSSAFKAAAFFVLLSMVLILGCITCFSLFFFCNTATVYKICAWMQL
LAALCLVLGCMIFPDGWDAETIRDMCGAKTGKYSLGDCSVRWAYILAIIGILNALILSFL
AFVLGNRQTD

Ligands and cofactors

ID	Name	Formula	Copies
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
PGW	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexade…	C40 H77 O10 P	3
D10	Decane	C10 H22	3
R16	Hexadecane	C16 H34	1
HEX	Hexane	C6 H14	3
PLM	Palmitic acid	C16 H32 O2	1
CLR	Cholesterol	C27 H46 O	1
PX2	1,2-dilauroyl-sn-glycero-3-phosphate	C27 H52 O8 P	1
A8W	Pregnenolone sulfate	C21 H32 O5 S	1

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

Primary citation

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, Megabody38 and pregnenolone sulfate. Kasaragod, V.B., 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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