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

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC2). Determined by electron microscopy at 3.2 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Lama glama
Chains: 10
Atoms: 18,975
Mol. weight: 453.82 kDa
Ligands: R16, PX2, NAG, CLR
Released: 2 Jul 2025

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

Secondary structure: helices and β-sheets

9FAV contains 87 α-helices and 103 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: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	35	1
β-strand	36-46	11	7
β-strand	50-51	2	7
β-strand	56-68	13	7
α-helix	70-72	3
α-helix	80-81	2
α-helix	87-90	4
β-strand	96-98	3	8
β-strand	101-106	6	7
β-strand	114-118	5	7
β-strand	123-135	13	7
α-helix	140-142	3
β-strand	147-156	10	8
β-strand	164-168	5	7
α-helix	171-173	3
β-strand	175-176	2	7
α-helix	178-180	3
β-strand	186-199	14	8
β-strand	204-216	13	8
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-241	4
α-helix	248-270	23
α-helix	280-303	24
α-helix	304-308	5
α-helix	422-445	24

Chain B: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	35	1
β-strand	36-41	6	1
β-strand	43	1	2
β-strand	44-51	8	1
β-strand	56-68	13	1
α-helix	70-72	3
β-strand	81-83	3	1
α-helix	85-90	6
β-strand	96-98	3	3
β-strand	101-106	6	1
β-strand	114-118	5	1
β-strand	123-135	13	1
β-strand	147	1	3
β-strand	150-156	7	3
β-strand	164-168	5	1
α-helix	171-173	3
β-strand	176	1	2
β-strand	186-199	14	3
β-strand	204-216	13	3
α-helix	220-221	2
α-helix	222-226	5
α-helix	227-240	14
α-helix	247-271	25
α-helix	280-302	23
α-helix	303-308	6
α-helix	422-445	24

Chain C: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	27-34	8
β-strand	51-66	16	11
β-strand	71-83	13	11
β-strand	95-98	4	11
α-helix	99	1
β-strand	111-113	3	12
β-strand	116	1	11
β-strand	120-121	2	11
β-strand	129-134	6	11
β-strand	138-150	13	11
β-strand	162-171	10	12
β-strand	179-190	12	11
α-helix	193-195	3
β-strand	202-214	13	12
β-strand	219-230	12	12
α-helix	235-236	2
α-helix	237-241	5
α-helix	242-251	10
α-helix	252-256	5
α-helix	262-281	20
α-helix	295-322	28
α-helix	375-379	5
α-helix	398-401	4
α-helix	402-426	25

Chain D: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
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	84	1
α-helix	85-90	6
β-strand	96-98	3	10
β-strand	101-106	6	9
β-strand	114-118	5	9
β-strand	123-135	13	9
α-helix	140-142	3
β-strand	147-156	10	10
β-strand	164-168	5	9
α-helix	171-174	4
β-strand	175	1	9
β-strand	186-198	13	10
β-strand	205-216	12	10
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-240	4
α-helix	247-269	23
α-helix	280-302	23
α-helix	303-307	5
α-helix	422-446	25

Chain E: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	35	1
β-strand	36-46	11	4
β-strand	50-51	2	4
β-strand	56-68	13	4
α-helix	70-72	3
β-strand	83	1	5
α-helix	85-89	5
β-strand	96-98	3	6
β-strand	101-106	6	4
β-strand	114-115	2	4
β-strand	116	1	5
β-strand	123-135	13	4
α-helix	140-142	3
β-strand	147-156	10	6
β-strand	164-168	5	4
β-strand	175-176	2	4
α-helix	178-180	3
β-strand	186-199	14	6
β-strand	204-216	13	6
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-241	4
α-helix	247-267	21
α-helix	280-306	27
α-helix	422-445	24

Chain F: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	20
β-strand	406-413	8	20
α-helix	415-417	3
β-strand	420-426	7	21
β-strand	433-438	6	21
β-strand	446-447	2	21
α-helix	449-451	3
β-strand	455-460	6	20
β-strand	465-470	6	20
α-helix	475-477	3
β-strand	479-486	8	21
α-helix	496-498	3
β-strand	501-502	2	21
β-strand	506-508	3	21

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	673-699	27

Chain K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	15
β-strand	408-413	6	15
α-helix	415-417	3
β-strand	421-427	7	16
β-strand	430-438	9	16
β-strand	445-447	3	16
α-helix	449-451	3
β-strand	458-459	2	17
β-strand	465	1	15
β-strand	466-467	2	17
β-strand	479-485	7	16
α-helix	496-498	3
β-strand	501-502	2	16
β-strand	506-508	3	16

2 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
Gamma-aminobutyric acid receptor subunit beta-3	A, B, D, E	protein	439	Homo sapiens	P28472 (AlphaFold model)
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2	C	protein	405	Homo sapiens	P18507 (AlphaFold model)
Neuroligin-2	H	protein	33	Homo sapiens	Q8NFZ4 (AlphaFold model)
LHFPL tetraspan subfamily member 4 protein	L	protein	185	Homo sapiens	Q7Z7J7 (AlphaFold model)
Megabody25	F, K, O	protein	522	Lama glama

Sequence of entity 1 (A, B, D, E), FASTA

>9FAV_1 Gamma-aminobutyric acid receptor subunit beta-3 (chains A, B, D, E)
MSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWR
DKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGL
RITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQFSI
VEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDASA
ARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFG
RGPQRQKKLAEKTAKAKNDRSKSESNRVDAHGNILLTSLEVHNEMNEVSGGIGDTRNSAI
SFDNSGIQYRKQSMPREGHGRFLGDRSLPHKKTHLRRRSSQLKIKIPDLTDVNAIDRWSR
IVFPFTFSLFNLVYWLYYV

Sequence of entity 2 (C), FASTA

>9FAV_2 Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2 (chains C)
GDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQTWYD
RRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLYTLR
LTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQFSFV
GLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDAVPA
RTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSNR
KPSKDKDKKKKNPAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCCFED
CRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYLG

Sequence of entity 3 (H), FASTA

>9FAV_3 Neuroligin-2 (chains H)
DSRDYSTELSVTVAVGASLLFLNILAFAALYYK

Sequence of entity 4 (L), FASTA

>9FAV_4 LHFPL tetraspan subfamily member 4 protein (chains L)
RNSRAIGVLWAIFTICFAIINVVVFIQPYWVGDSVSTPKPGYFGLFHYCVGSGLAGRELT
CRGSFTDFSTIPSSAFKAAAFFVLLSMVLILGCITCFSLFFFCNTATVYKICAWMQLLAA
LCLVLGCMIFPDGWDAETIRDMCGAKTGKYSLGDCSVRWAYILAIIGILNALILSFLAFV
LGNRQ

Sequence of entity 5 (F, K, O), FASTA

>9FAV_5 Megabody25 (chains F, K, O)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSR
LLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGY
AVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLS
IEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGHTFNYPI
MGWFRQAPGKEREFVGAISWSGGSTSYADSVKDRFTISRDNAKNTVYLEMNNLKPEDTAV
YYCAAKGRYSGGLYYPTNYDYWGQGTQVTVSSHHHHHHEPEA

Ligands and cofactors

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

Primary citation

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC2). Kasaragod, V.B., Aricescu, A.R. To be published.

Other PDB entries of the same protein (UniProt P28472 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7A5V 1.7 Å, CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3…
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…
6QFA 2.49 Å, CryoEM structure of a beta3K279T GABA(A)R homomer in complex with histamine and megabody…
7QN5 2.5 Å, Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R in…
9FAS 2.5 Å, CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with…
9FEU 2.5 Å, Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the…
9FFU 2.5 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…
9G2E 2.5 Å, Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived desensitised…
9QJS 2.52 Å, GABA-A receptor a2b3 (1:4) + a2NB16(silent) + b3Mb125 + GABA
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…

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