9FF2: Beta3 homomeric GABA(A) receptor

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state (C1). Determined by electron microscopy at 2.8 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 14,680
Mol. weight: 238.87 kDa
Ligands: D10, HSM, NAG
Released: 4 Jun 2025

Explore 9FF2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FF2 contains 65 α-helices and 65 β-strands across 5 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: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	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	2
β-strand	101-106	6	1
β-strand	110	1	3
β-strand	114-118	5	1
β-strand	123-135	13	1
α-helix	140-142	3
β-strand	147-156	10	2
β-strand	164-168	5	1
α-helix	171-173	3
β-strand	175-176	2	1
α-helix	178-180	3
β-strand	186-200	15	2
β-strand	203-216	14	2
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-238	12
α-helix	239-241	3
α-helix	247-271	25
α-helix	278-279	2
α-helix	280-305	26
α-helix	310-446	30

Chain B: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
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	85-90	6
β-strand	96-98	3	5
β-strand	101-106	6	4
β-strand	110	1	2
β-strand	114-118	5	4
β-strand	123-135	13	4
β-strand	147-156	10	5
β-strand	164-168	5	4
α-helix	171-174	4
β-strand	175-176	2	4
α-helix	178-180	3
β-strand	186-200	15	5
β-strand	203-216	14	5
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-238	12
α-helix	247-270	24
α-helix	280-305	26
α-helix	310-445	29

Chain C: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	6
β-strand	56-68	13	6
α-helix	70-72	3
β-strand	81-83	3	6
α-helix	85-90	6
β-strand	96-98	3	7
β-strand	101-106	6	6
β-strand	110	1	5
β-strand	114-118	5	6
β-strand	123-135	13	6
β-strand	147-156	10	7
β-strand	164-168	5	6
α-helix	171-173	3
β-strand	175-176	2	6
α-helix	178-180	3
β-strand	186-200	15	7
β-strand	203-216	14	7
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-238	12
α-helix	239-241	3
α-helix	247-271	25
α-helix	280-305	26
α-helix	310-445	29

Chain D: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	8
β-strand	56-68	13	8
α-helix	70-72	3
β-strand	81-83	3	8
α-helix	85-90	6
β-strand	96-98	3	9
β-strand	101-106	6	8
β-strand	110	1	7
β-strand	114-118	5	8
β-strand	123-135	13	8
α-helix	140-142	3
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	186-200	15	9
β-strand	203-216	14	9
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-241	4
α-helix	247-271	25
α-helix	280-305	26
α-helix	310-445	29

Chain E: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	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	3
β-strand	101-106	6	10
β-strand	110	1	9
β-strand	114-118	5	10
β-strand	123-135	13	10
β-strand	147-156	10	3
β-strand	164-168	5	10
α-helix	171-173	3
β-strand	175-176	2	10
β-strand	186-200	15	3
β-strand	203-216	14	3
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-238	12
α-helix	239-241	3
α-helix	247-271	25
α-helix	280-305	26
α-helix	310-446	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit beta-3	A, B, C, D, E	protein	395	Homo sapiens	P28472 (AlphaFold model)

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

>9FF2_1 Gamma-aminobutyric acid receptor subunit beta-3 (chains A, B, C, D, E)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPDYDIPTTENLYFQGTGQSVNDP
GNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQY
WRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLY
GLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQF
SIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDA
SAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIF
FSQPARAAAIDRWSRIVFPFTFSLFNLVYWLYYVN

Ligands and cofactors

ID	Name	Formula	Copies
D10	Decane	C10 H22	15
HSM	Histamine	C5 H9 N3	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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

Primary citation

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state (C1). Mihaylov, D.B., Malinauskas, T., 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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