9CXA: Gamma-aminobutyric acid receptor subunit beta-2

Native human GABAA receptor of beta2-alpha1-beta3-alpha1-gamma2 assembly. Determined by electron microscopy at 3.04 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.04 Å
Organisms: Homo sapiens, Mus musculoides
Chains: 9
Atoms: 16,521
Mol. weight: 436.18 kDa
Ligands: NAG, POV, PIO, ABU
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

9CXA contains 56 α-helices and 126 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: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	28	1
α-helix	35	1
β-strand	36-47	12	1
β-strand	51	1	1
β-strand	56-68	13	1
β-strand	81-83	3	1
α-helix	85-89	5
β-strand	96-98	3	2
β-strand	101-106	6	1
β-strand	114-118	5	1
β-strand	123-135	13	1
β-strand	147-156	10	2
β-strand	164-168	5	1
β-strand	175-176	2	1
β-strand	186-199	14	2
β-strand	204-216	13	2
α-helix	218-221	4
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-240	4
α-helix	247-266	20
α-helix	269-271	3
α-helix	280-303	24
α-helix	304-308	5
α-helix	463-485	23

Chain B: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-54	16	3
β-strand	59-70	12	3
β-strand	71	1	4
α-helix	73-75	3
β-strand	83-86	4	5
α-helix	90-92	3
β-strand	99-101	3	6
β-strand	104	1	3
β-strand	108-109	2	3
β-strand	113	1	2
β-strand	117	1	3
β-strand	119-122	4	5
β-strand	126	1	4
β-strand	129-138	10	3
β-strand	150-159	10	6
β-strand	167-171	5	3
α-helix	175-177	3
β-strand	179-181	3	3
β-strand	186	1	3
β-strand	191-204	14	6
β-strand	209-221	13	6
α-helix	225-227	3
α-helix	231-241	11
α-helix	243-245	3
α-helix	252-274	23
α-helix	285-308	24
α-helix	391-416	26

Chain C: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
α-helix	35	1
β-strand	36-51	16	7
β-strand	56-66	11	7
β-strand	67-68	2	8
α-helix	70-72	3
β-strand	81	1	8
α-helix	85-89	5
β-strand	96-98	3	9
β-strand	101-106	6	7
β-strand	114-115	2	7
β-strand	118	1	8
β-strand	123-124	2	8
β-strand	127-135	9	7
β-strand	147-156	10	9
β-strand	164-168	5	7
α-helix	171-173	3
β-strand	175-176	2	7
β-strand	186-200	15	9
β-strand	203-216	14	9
α-helix	217	1
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-240	4
α-helix	247-268	22
α-helix	280-306	27
α-helix	421-445	25

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-54	16	10
β-strand	59-71	13	10
α-helix	73-75	3
β-strand	84-86	3	10
β-strand	99-101	3	11
β-strand	104-109	6	10
β-strand	117	1	10
β-strand	119-121	3	10
β-strand	126-138	13	10
β-strand	150-159	10	11
β-strand	167-171	5	10
β-strand	179-181	3	10
β-strand	191-204	14	11
β-strand	209-221	13	11
α-helix	225-226	2
α-helix	227-231	5
α-helix	232-243	12
α-helix	252-272	21
α-helix	285-309	25
α-helix	391-415	25

Chain E: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	27-34	8
α-helix	43	1
α-helix	50	1
β-strand	51-66	16	12
β-strand	71-83	13	12
α-helix	85-87	3
β-strand	95-98	4	12
α-helix	100-105	6
β-strand	111-113	3	13
β-strand	116-121	6	12
β-strand	129-134	6	12
β-strand	138-150	13	12
β-strand	162-165	4	13
β-strand	168-171	4	13
β-strand	179-190	12	12
β-strand	201-214	14	13
β-strand	219-231	13	13

Chain I: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	14
β-strand	7	1	15
β-strand	10-12	3	16
β-strand	19-20	2	17
β-strand	22	1	15
β-strand	23-24	2	18
β-strand	25	1	14
β-strand	33-38	6	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-65	4	17
β-strand	70-71	2	18
β-strand	72-75	4	17
α-helix	80-82	3
β-strand	85-90	6	19
β-strand	96-97	2	19
β-strand	101	1	19
β-strand	102-104	3	16

Chain J: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	20
β-strand	10-11	2	21
β-strand	17-25	9	20
β-strand	34-39	6	22
β-strand	45-51	7	22
β-strand	58-60	3	22
α-helix	62-64	3
β-strand	65	1	20
β-strand	68-73	6	20
β-strand	78-84	7	20
α-helix	88-90	3
β-strand	93-98	6	22
β-strand	108	1	22
β-strand	112-113	2	22
β-strand	114-115	2	21

Chain K: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	23
α-helix	7-9	3
β-strand	10-12	3	24
β-strand	18	1	23
β-strand	21-25	5	23
β-strand	34-39	6	25
β-strand	45-52	8	25
β-strand	57-60	4	25
α-helix	62-64	3
β-strand	68-73	6	23
β-strand	78-83	6	23
β-strand	93-99	7	25
β-strand	105-108	4	25
β-strand	112-113	2	25
β-strand	114-116	3	24

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 beta-2	A	protein	512	Homo sapiens	P47870 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-1	B, D	protein	456	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	C	protein	473	Homo sapiens	P28472 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	E	protein	475	Homo sapiens	P18507 (AlphaFold model)
Kappa Fab_1F4 Light Chain	I, L	protein	258	Mus musculoides
IgG2b Fab_1F4 Heavy Chain	J, K	protein	454	Homo sapiens

Sequence of entity 1 (A), FASTA

>9CXA_1 Gamma-aminobutyric acid receptor subunit beta-2 (chains A)
MWRVRKRGYFGIWSFPLIIAAVCAQSVNDPSNMSLVKETVDRLLKGYDIRLRPDFGGPPV
AVGMNIDIASIDMVSEVNMDYTLTMYFQQAWRDKRLSYNVIPLNLTLDNRVADQLWVPDT
YFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIES
YGYTTDDIEFYWRGDDNAVTGVTKIELPQFSIVDYKLITKKVVFSTGSYPRLSLSFKLKR
NIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLTMTTINTHLRETLPKIP
YVKAIDMYLMGCFVFVFMALLEYALVNYIFFGRGPQRQKKAAEKAASANNEKMRLDVNKI
FYKDIKQNGTQYRSLWDPTGNLSPTRRTTNYDFSLYTMDPHENILLSTLEIKNEMATSEA
VMGLGDPRSTMLAYDASSIQYRKAGLPRHSFGRNALERHVAQKKSRLRRRASQLKITIPD
LTDVNAIDRWSRIFFPVVFSFFNIVYWLYYVN

Sequence of entity 2 (B, D), FASTA

>9CXA_2 Gamma-aminobutyric acid receptor subunit alpha-1 (chains B, D)
MRKSPGLSDCLWAWILLLSTLTGRSYGQPSLQDELKDNTTVFTRILDRLLDGYDNRLRPG
LGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASK
IWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLYTMRLTVRAECPMHLEDFPMDAHAC
PLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVM
TTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISA
RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVPEKPKKVKDP
LIKKNNTYAPTATSYTPNLARGDPGLATIAKSATIEPKEVKPETKPPEPKKTFNSVSKID
RLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 3 (C), FASTA

>9CXA_3 Gamma-aminobutyric acid receptor subunit beta-3 (chains C)
MWGLAGGRLFGIFSAPVLVAVVCCAQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP
VCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPD
TYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIE
SYGYTTDDIEFYWRGGDKAVTGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLK
RNIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLTMTTINTHLRETLPKI
PYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAEKTAKAKNDRSKSESNR
VDAHGNILLTSLEVHNEMNEVSGGIGDTRNSAISFDNSGIQYRKQSMPREGHGRFLGDRS
LPHKKTHLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 4 (E), FASTA

>9CXA_4 Gamma-aminobutyric acid receptor subunit gamma-2 (chains E)
MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK
VPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQT
WYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLY
TLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQF
SFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDA
VPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFV
SNRKPSKDKDKKKKNPLLRMFSFKAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGK
DCASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYL

Sequence of entity 5 (I, L), FASTA

>9CXA_5 Kappa Fab_1F4 Light Chain (chains I, L)
MGWSCIILFLVATATGVHSNIVMTQSPKSMSMSVGERVTLSCKASEYVGTYVSWYQQKPE
QSPKLLIYGASNRYTGVPDRFTGSGSATDFTLTIGSVQAEDLADYHCGQSYSYPTFGAGT
KLELKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECDYKD
HDGDYKDHDIDYKDDDDK

Sequence of entity 6 (J, K), FASTA

>9CXA_6 IgG2b Fab_1F4 Heavy Chain (chains J, K)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMYWVKQRPEQGLEWIGRIDPANGDTKY
DPKFQGKATITTDTFSNTAYLQLSSLTSEDTAVYYCARKGLRWAMDYWGQGTSVTVSTAK
TTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPN
LEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHR
EDYNSTIRVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPP
PAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMK
TSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	2
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
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2

Primary citation

Resolving native GABA A receptor structures from the human brain. Zhou, J., Noviello, C.M., Teng, J. et al. Nature (2025) 638:562-568. DOI 10.1038/s41586-024-08454-1 · PubMed

Other PDB entries of the same protein (UniProt P47870 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
8SGO 2.65 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus pregnenolone…
8SID 2.71 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus…
8VQY 2.82 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus methaqualone
6X40 2.86 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus picrotoxin
8DD2 2.9 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus Zolpidem
8DD3 2.9 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus DMCM
9CRS 2.9 Å, Native human GABAA receptor of beta2-alpha1-beta2-alpha1-gamma2 assembly
6X3X 2.92 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus diazepam
9DRX 2.95 Å, Human GABAA receptor of beta2-alpha1-beta2-alpha1-gamma2 subtype in complex with GABA…
8SI9 2.98 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus…

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