9HNT: A5b3 GABAAR

a5b3 GABAAR bound to Etomidate, GABA, and Mb25 in a desensitized state in saposin nanodiscs. Determined by electron microscopy at 3.32 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 3.32 Å
Organisms: Aequorea victoria, Homo sapiens, Escherichia coli
Chains: 6
Atoms: 15,197
Mol. weight: 431.48 kDa
Ligands: NAG, ABU, V8D
Released: 24 Dec 2025

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

Secondary structure: helices and β-sheets

9HNT contains 72 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, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
β-strand	41-56	16	1
β-strand	61-73	13	1
α-helix	75-77	3
β-strand	85-86	2	1
α-helix	90-94	5
β-strand	101-103	3	2
β-strand	106-111	6	1
β-strand	119-124	6	1
β-strand	128-140	13	1
α-helix	148-150	3
β-strand	152-161	10	2
β-strand	169-173	5	1
β-strand	181-183	3	1
β-strand	193-207	15	2
β-strand	210-223	14	2
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-243	10
α-helix	244-248	5
α-helix	254-275	22
α-helix	276-278	3
α-helix	287-315	29
α-helix	326-351	26

Chain B: 15 helices, 12 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	82-83	2	3
α-helix	85-90	6
β-strand	96-98	3	4
β-strand	101-106	6	3
β-strand	114-118	5	3
β-strand	123-135	13	3
α-helix	140-142	3
β-strand	147-156	10	4
β-strand	164-168	5	3
α-helix	171-174	4
β-strand	175-176	2	3
α-helix	178-180	3
β-strand	186-200	15	4
β-strand	203-216	14	4
α-helix	217	1
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-240	3
α-helix	247-269	23
α-helix	280-307	28
α-helix	550-582	33

Chain C: 16 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	85-89	5
β-strand	96-98	3	6
β-strand	101-106	6	5
β-strand	114-118	5	5
β-strand	123-135	13	5
α-helix	140-145	6
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	182	1	6
β-strand	186-199	14	6
β-strand	204-216	13	6
α-helix	217	1
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-241	5
α-helix	247-269	23
α-helix	278-279	2
α-helix	280-307	28
α-helix	551-583	33

Chain D: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
β-strand	41-56	16	7
β-strand	61-73	13	7
α-helix	75-77	3
β-strand	85-88	4	7
α-helix	90-92	3
β-strand	102-103	2	8
β-strand	106-111	6	7
β-strand	119-124	6	7
β-strand	128-140	13	7
α-helix	148-150	3
β-strand	152-160	9	8
β-strand	169-173	5	7
α-helix	178-180	3
β-strand	181-183	3	7
β-strand	188	1	7
β-strand	193-208	16	8
β-strand	210-223	14	8
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-244	11
α-helix	245-248	4
α-helix	254-275	22
α-helix	289-313	25
α-helix	324-350	27

Chain E: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	28	1
α-helix	35	1
β-strand	36-51	16	9
β-strand	56-68	13	9
α-helix	70-72	3
β-strand	82-83	2	9
α-helix	85-89	5
β-strand	96-98	3	10
β-strand	101-106	6	9
β-strand	108	1	11
β-strand	112	1	11
β-strand	114-117	4	9
β-strand	123-135	13	9
α-helix	140-142	3
β-strand	147-148	2	10
β-strand	151-156	6	10
β-strand	164-168	5	9
α-helix	171-173	3
β-strand	175-176	2	9
β-strand	186-200	15	10
β-strand	203-216	14	10
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-240	4
α-helix	247-269	23
α-helix	280-306	27
α-helix	556-581	26

Chain P: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11	1	13
β-strand	405-412	8	12
α-helix	415-417	3
β-strand	420-425	6	14
β-strand	426	1	15
β-strand	433-439	7	14
β-strand	446-447	2	14
β-strand	455-460	6	12
β-strand	465-470	6	12
α-helix	475-477	3
β-strand	480	1	15
β-strand	483-486	4	14
α-helix	496-498	3
β-strand	499-502	4	14
β-strand	507	1	15
β-strand	509	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5	A, D	protein	679	Aequorea victoria, Homo sapiens	P31644 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit…	B, C, E	protein	623	Homo sapiens, Aequorea victoria	P28472 (AlphaFold model)
Megabody 25	P	protein	541	Escherichia coli

Sequence of entity 1 (A, D), FASTA

>9HNT_1 Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5 (chains A, D)
MRKSPGLSDCLWAWILLLSTLTGRSYGQMSKGEELFTGVVPILVELDGDVNGHKFSVRGE
GEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGY
VQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYI
TADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPN
EKRDHMVLLEFVTAAGITHGMDELYKAANALAAWSHPQFEKGGGSGGGSGGGSWSHPQFE
KSSSNNNNNENLYFQAMPTSSVKDETNDNITIFTRILDGLLDGYDNRLRPGLGERITQVR
TDIYVTSFGPVSDTEMEYTIDVFFRQSWKDERLRFKGPMQRLPLNNLLASKIWTPDTFFH
NGKKSIAHNMTTPNKLLRLEDDGTLLYTMRLTISAECPMQLEDFPMDAHACPLKFGSYAY
PNSEVVYVWTNGSTKSVVVAEDGSRLNQYHLMGQTVGTENISTSTGEYTIMTAHFHLKRK
IGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAY
ATAMDWFIAVCYAFVFSALIEFATVNYFTKSQPARAASISKIDKMSRIVFPVLFGTFNLV
YWATYLNREPVIKGAASPK

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

>9HNT_2 Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein (chains B, C, E)
MWGLAGGRLFGIFSAPVLVAVVCCAQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP
VCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPD
TYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIE
SYGYTTDDIEFYWRGGDKAVTGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLK
RNIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLTMTTINTHLRETLPKI
PYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFSQPGRAMVSKGEELFTGVVPILVEMDGD
VNGRKFSVRGVGEGDATHGKLTLKFICTSGKLPVPWPTLVTTLSYGVQCFSRYPDHMKQH
DFFKSAMPEGYVQERTIFFKDDGSYKTRAEVKFEGDTLVNRIVLKGTDFKEDGNILGHKL
EYNMNVGNVYITADKQKNGIKANFEIRHNVEDGGVQLADHYQQNTPIGDGSVLLPDNHYL
SVQVKLSKDPNEKRDHMVLLEFRTAAGITPGMDELYKGRAAAIDRWSRIVFPFTFSLFNL
VYWLYYVNSRENLYFQAHHHHHH

Sequence of entity 3 (P), FASTA

>9HNT_3 Megabody 25 (chains P)
MKKIWLALAGLVLAFSASAQVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTL
KDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQET
QQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGH
LKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQN
LANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAY
QATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNG
THSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSK
YGSLRLSCAASGHTFNYPIMGWFRQAPGKEREFVGAISWSGGSTSYADSVKDRFTISRDN
AKNTVYLEMNNLKPEDTAVYYCAAKGRYSGGLYYPTNYDYWGQGTQVTVSSHHHHHHEPE
A

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
V8D	Etomidate	C14 H16 N2 O2	2

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

Primary citation

Structural basis for activation and potentiation in a human alpha 5 beta 3 GABA A receptor. Cowgill, J., Fan, C., Steyaert, J. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-74279-3 · PubMed

Other PDB entries of the same protein (UniProt P31644 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8BHG 2.39 Å, GABA-A receptor a5 heteromer - a5V2 - Bretazenil
8BHB 2.54 Å, GABA-A receptor a5 homomer - a5V3 - RO154513
8BGI 2.56 Å, GABA-A receptor a5 homomer - a5V1 - Flumazenil
8BHA 2.67 Å, GABA-A receptor a5 homomer - a5V3 - Basmisanil - HR
8BHI 2.67 Å, GABA-A receptor a5 homomer - a5V3 - RO5211223
8BHO 2.93 Å, GABA-A receptor a5 homomer - a5V3 - L655708
8BHM 2.95 Å, GABA-A receptor a5 homomer - a5V3 - DMCM
9HNS 3.1 Å, a5b3 GABAAR bound to GABA and Mb25 in a desensitized state in saposin nanodiscs after…
9RL5 3.1 Å, a5b3 GABAAR bound to Topiramate, GABA, and Mb25 in a desensitized state in saposin…
9RPB 3.1 Å, a5b3 GABAAR bound to GABA, and Mb25 in a desensitized state in saposin nanodiscs,…
9HAA 3.14 Å, a5b3 GABAA Receptor resting state
9HNR 3.17 Å, a5b3 GABAA Receptor in 1 a5 to 4 b3 stoichiometry in desensitized state

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