9QK1: Gamma-aminobutyric acid receptor subunit alpha-2

GABA-A receptor a2b3 (1:4) + a2NB06(silent) + b3Mb125 + GABA. Determined by electron microscopy at 3.05 Å resolution. Released 26 Aug 2026.

Method: Electron microscopy
Resolution: 3.05 Å
Organisms: Homo sapiens, Escherichia coli, Lama glama
Chains: 9
Atoms: 17,635
Mol. weight: 312.25 kDa
Ligands: NAG, ABU, HSM
Released: 26 Aug 2026

Explore 9QK1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QK1 contains 75 α-helices and 106 β-strands across 9 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: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
β-strand	38-53	16	1
β-strand	58-70	13	1
α-helix	72-74	3
β-strand	82-85	4	1
α-helix	87-92	6
β-strand	98-100	3	2
β-strand	103	1	1
β-strand	107-108	2	1
β-strand	116-121	6	1
β-strand	125-137	13	1
β-strand	149-158	10	2
β-strand	166-170	5	1
α-helix	175-177	3
β-strand	178-180	3	1
β-strand	190-203	14	2
β-strand	208-220	13	2
α-helix	223-225	3
α-helix	226-230	5
α-helix	231-241	11
α-helix	242-245	4
α-helix	251-272	22
α-helix	284-312	29
α-helix	389-411	23

Chain B: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
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
β-strand	147-148	2	4
β-strand	151-156	6	4
β-strand	164-168	5	3
α-helix	171-173	3
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	219-221	3
α-helix	222-226	5
α-helix	227-241	15
α-helix	247-263	17
α-helix	266-271	6
α-helix	280-302	23
α-helix	418-445	28

Chain C: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	35	1
β-strand	36-51	16	5
β-strand	56-68	13	5
α-helix	70-72	3
α-helix	80	1
β-strand	81-83	3	5
α-helix	85-90	6
β-strand	96-98	3	6
β-strand	101-106	6	5
β-strand	114-118	5	5
β-strand	123-135	13	5
β-strand	147-156	10	6
β-strand	164-168	5	5
β-strand	175-176	2	5
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	227-236	10
α-helix	238-241	4
α-helix	247-265	19
α-helix	280-307	28
α-helix	421-446	26

Chain D: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
α-helix	35	1
β-strand	36-51	16	7
β-strand	56-68	13	7
α-helix	70-72	3
β-strand	82-83	2	7
α-helix	85-90	6
β-strand	96-97	2	8
β-strand	101-106	6	7
β-strand	114-118	5	7
β-strand	123-135	13	7
β-strand	147-148	2	8
β-strand	151-156	6	8
β-strand	164-168	5	7
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	227-241	15
α-helix	247-270	24
α-helix	280-306	27
α-helix	419-427	9
α-helix	430-445	16

Chain E: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	35	1
β-strand	36-46	11	9
β-strand	50-51	2	9
β-strand	56-68	13	9
α-helix	70-72	3
β-strand	82-83	2	9
α-helix	85-90	6
β-strand	96-98	3	10
β-strand	101-106	6	9
β-strand	114-117	4	9
β-strand	123-135	13	9
β-strand	147-148	2	10
β-strand	151-156	6	10
β-strand	164-168	5	9
β-strand	175-176	2	9
α-helix	178-180	3
β-strand	186-199	14	10
β-strand	204-216	13	10
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-240	4
α-helix	247-262	16
α-helix	268-271	4
α-helix	278-279	2
α-helix	280-307	28
α-helix	423-445	23

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-13	4	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	46-51	6	12
β-strand	59-60	2	12
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	112-113	2	12
β-strand	117-122	6	12

Chain G: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	13
β-strand	405-413	9	13
α-helix	415-417	3
β-strand	420-426	7	14
β-strand	433-439	7	14
β-strand	445-447	3	14
α-helix	449-451	3
β-strand	457-460	4	13
β-strand	465-470	6	13
β-strand	479-486	8	14
α-helix	496-498	3
β-strand	499-502	4	14
β-strand	506-508	3	14

Chain H: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	406-410	5	15
α-helix	415-417	3
β-strand	420-426	7	16
α-helix	431-432	2
β-strand	433-439	7	16
β-strand	445-447	3	16
α-helix	449-451	3
β-strand	457-460	4	15
β-strand	465-469	5	15
β-strand	479-486	8	16
α-helix	496-498	3
β-strand	499-502	4	16
β-strand	506-508	3	16

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
Gamma-aminobutyric acid receptor subunit alpha-2	A	protein	365	Homo sapiens	P47869 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562	B, C, D, E	protein	451	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P28472 (AlphaFold model)
a2NB06	F	protein	133	Lama glama
Mb125	G, H, I	protein	133	Lama glama

Sequence of entity 1 (A), FASTA

>9QK1_1 Gamma-aminobutyric acid receptor subunit alpha-2 (chains A)
NIQEDEAKNNITIFTRILDRLLDGYDNRLRPGLGDSITEVFTNIYVTSFGPVSDTDMEYT
IDVFFRQKWKDERLKFKGPMNILRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRI
QDDGTLLYTMRLTVQAECPMHLEDFPMDAHSCPLKFGSYAYTTSEVTYIWTYNASDSVQV
APDGSRLNQYDLLGQSIGKETIKSSTGEYTVMTAHFHLKRKIGYFVIQTYLPCIMTVILS
QVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSAL
IEFATVNYFTKSQPARAAKIDRMSRIVFPVLFGTFNLVYWATYLNREPVLGVSPGTTETS
QVAPA

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

>9QK1_2 Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562 (chains B, C, D, E)
QSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLT
MYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHP
DGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVER
IELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSF
WINYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYA
FVNYIFFSQPAGTADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPK
LEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLT
GRAAAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 3 (F), FASTA

>9QK1_3 a2NB06 (chains F)
QVQLVESGGGLVQAGGSLRLSCAASGRTFSSYTMGWFRQAPGKEREFVAGDSWSGGSTYY
ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAASLAGGPPIADEYNYWGQGTQVT
VSSHHHHHHEPEA

Sequence of entity 4 (G, H, I), FASTA

>9QK1_4 Mb125 (chains G, H, I)
QVQLVESGGGLVQGSLRLSCAASGHTFNYPIMGWFRQAPGKEREFVGAISWSGGSTSYAD
SVKDRFTISRDNAKNTVYLEMNNLKPEDTAVYYCAAKGRYSGGLYYPTNYDYWGQGTQVT
VSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	1
HSM	Histamine	C5 H9 N3	3

Primary citation

Determining the molecular and physiological actions of subtype-selective nanobodies of GABA A receptors. Gonzalez-Prada, J.E., Liu, S., Shang, C. et al. Sci Adv (2026) 12:eaeg3548-eaeg3548. DOI 10.1126/sciadv.aeg3548 · PubMed

Other PDB entries of the same protein (UniProt P47869 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QJS 2.52 Å, GABA-A receptor a2b3 (1:4) + a2NB16(silent) + b3Mb125 + GABA
9QJX 2.7 Å, GABA-A receptor a2b3g2 + a2NB00(PAM) + GABA
9QJY 2.78 Å, GABA-A receptor a2b3g2 + a2NB04(silent) + GABA
9QJR 2.92 Å, GABA-A receptor a2b3 (1:4) + a2NB29(near-silent) + b3Mb125 + GABA
9QK0 3.01 Å, GABA-A receptor a2b3g2 + a2NB25(inhibitor)
9CRV 3.18 Å, Native human GABAA receptor of beta2-alpha1-gamma2-beta2-alpha2 assembly
9CT0 3.19 Å, Native human GABAA receptor of beta2-alpha1-beta2-alpha2-gamma2 assembly
9CX7 3.3 Å, Native human GABAA receptor of beta3-alpha1-gamma2-beta3-alpha2 assembly
9CXC 3.3 Å, Native human GABAA receptor of beta3-alpha1-gamma2-beta2-alpha2 assembly
9CXB 3.33 Å, Native human GABAA receptor of beta2-alpha1-beta1-alpha2-gamma2 assembly
9CSB 3.34 Å, Native human GABAA receptor of beta3-alpha1-beta2-alpha2-gamma2 assembly
9CTV 3.36 Å, Native human GABAA receptor of beta2-alpha1-gamma2-beta1-alpha2 assembly

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