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

Native human GABAA receptor of beta2-alpha1-beta1-beta1-gamma2 assembly. Determined by electron microscopy at 3.36 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.36 Å
Organisms: Homo sapiens, Mus musculus
Chains: 7
Atoms: 15,403
Mol. weight: 335.08 kDa
Ligands: ABU, NAG, PIO
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

9CXD contains 58 α-helices and 104 β-strands across 7 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, 12 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
α-helix	35	1
β-strand	36-51	16	1
β-strand	56-68	13	1
β-strand	82-83	2	1
α-helix	85-89	5
β-strand	97-98	2	2
β-strand	101-106	6	1
β-strand	114-118	5	1
β-strand	123-135	13	1
α-helix	140-142	3
β-strand	147-155	9	2
β-strand	164-168	5	1
α-helix	171-173	3
β-strand	175-176	2	1
β-strand	186-200	15	2
β-strand	203-216	14	2
α-helix	217	1
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-238	12
α-helix	247-269	23
α-helix	280-303	24
α-helix	304-308	5
α-helix	462-485	24

Chain B: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
β-strand	41-44	4	3
β-strand	45-54	10	4
β-strand	59-64	6	4
β-strand	67-69	3	3
β-strand	71	1	5
α-helix	73-75	3
β-strand	83-86	4	3
α-helix	88-90	3
β-strand	99-101	3	6
β-strand	104	1	4
β-strand	108-109	2	4
β-strand	117-122	6	3
β-strand	126	1	5
β-strand	127-131	5	3
β-strand	133-138	6	4
β-strand	150-159	10	6
β-strand	169-171	3	3
α-helix	175-177	3
β-strand	179-181	3	4
β-strand	186	1	4
β-strand	193-204	12	6
β-strand	209-220	12	6
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-241	10
α-helix	244-246	3
α-helix	252-274	23
α-helix	285-310	26
α-helix	391-415	25

Chain C: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	35	1
β-strand	36-51	16	7
β-strand	56-66	11	7
β-strand	68	1	8
β-strand	82-83	2	9
α-helix	88-90	3
β-strand	97-98	2	10
β-strand	101-106	6	7
β-strand	114-115	2	7
β-strand	116-117	2	9
β-strand	118	1	11
β-strand	123	1	8
β-strand	124	1	11
β-strand	127-128	2	7
β-strand	130-135	6	7
β-strand	147-155	9	10
β-strand	164-168	5	7
β-strand	175-176	2	7
β-strand	186-195	10	10
β-strand	198-200	3	12
β-strand	203-205	3	12
β-strand	207-216	10	10
α-helix	221	1
α-helix	222-226	5
α-helix	227-236	10
α-helix	238-240	3
α-helix	247-266	20
α-helix	280-305	26
α-helix	424-428	5
α-helix	432-444	13

Chain D: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
α-helix	35	1
β-strand	36-51	16	13
β-strand	56-66	11	13
β-strand	67-68	2	14
β-strand	81	1	14
α-helix	85-87	3
β-strand	97-98	2	15
β-strand	101-106	6	13
β-strand	114-115	2	13
β-strand	118	1	14
β-strand	123-124	2	14
β-strand	127-135	9	13
β-strand	147-155	9	15
β-strand	164-168	5	13
β-strand	176	1	13
β-strand	187-199	13	15
β-strand	204-215	12	15
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-237	11
α-helix	238-241	4
α-helix	247-266	20
α-helix	269-271	3
α-helix	280-305	26
α-helix	422-447	26

Chain E: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
β-strand	51-62	12	16
β-strand	66	1	17
β-strand	71	1	17
β-strand	74-83	10	16
α-helix	85-87	3
β-strand	96-98	3	16
α-helix	102-105	4
β-strand	112-113	2	18
β-strand	116-121	6	16
β-strand	129	1	16
β-strand	131-133	3	16
β-strand	138-149	12	16
β-strand	150	1	17
β-strand	162-170	9	18
β-strand	179-190	12	16
β-strand	201-215	15	18
β-strand	218-231	14	18
α-helix	235-236	2
α-helix	237-241	5
α-helix	242-253	12
α-helix	262-286	25
α-helix	295-320	26
α-helix	409-432	24

Chain I: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10	1	20
β-strand	19-25	7	19
β-strand	33-37	5	21
β-strand	45-49	5	21
β-strand	53-54	2	21
α-helix	55	1
β-strand	62-65	4	19
β-strand	71-75	5	19
β-strand	85-86	2	20
β-strand	87-90	4	21
β-strand	96	1	21
β-strand	101-102	2	20

Chain J: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
β-strand	10-12	3	23
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	34-39	6	23
β-strand	45-52	8	23
β-strand	57-60	4	23
β-strand	68-73	6	22
β-strand	78-83	6	22
α-helix	88-90	3
β-strand	92-98	7	23
β-strand	108	1	23
β-strand	112-116	5	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit beta-2	A	protein	487	Homo sapiens	P47870 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-1	B	protein	429	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-1	C, D	protein	449	Homo sapiens	P18505 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	E	protein	436	Homo sapiens	P18507 (AlphaFold model)
Kappa Fab_1F4 Light Chain	I	protein	213	Mus musculus
IgG2b Fab_1F4 Heavy Chain	J	protein	454	Mus musculus

Sequence of entity 1 (A), FASTA

>9CXD_1 Gamma-aminobutyric acid receptor subunit beta-2 (chains A)
SVNDPSNMSLVKETVDRLLKGYDIRLRPDFGGPPVAVGMNIDIASIDMVSEVNMDYTLTM
YFQQAWRDKRLSYNVIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPD
GTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGDDNAVTGVTKI
ELPQFSIVDYKLITKKVVFSTGSYPRLSLSFKLKRNIGYFILQTYMPSILITILSWVSFW
INYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFMALLEYAL
VNYIFFGRGPQRQKKAAEKAASANNEKMRLDVNKIFYKDIKQNGTQYRSLWDPTGNLSPT
RRTTNYDFSLYTMDPHENILLSTLEIKNEMATSEAVMGLGDPRSTMLAYDASSIQYRKAG
LPRHSFGRNALERHVAQKKSRLRRRASQLKITIPDLTDVNAIDRWSRIFFPVVFSFFNIV
YWLYYVN

Sequence of entity 2 (B), FASTA

>9CXD_2 Gamma-aminobutyric acid receptor subunit alpha-1 (chains B)
QPSLQDELKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEY
TIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLR
ITEDGTLLYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVV
VAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVIL
SQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSA
LIEFATVNYFTKRGYAWDGKSVVPEKPKKVKDPLIKKNNTYAPTATSYTPNLARGDPGLA
TIAKSATIEPKEVKPETKPPEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWATYLNREP
QLKAPTPHQ

Sequence of entity 3 (C, D), FASTA

>9CXD_3 Gamma-aminobutyric acid receptor subunit beta-1 (chains C, D)
HSTNEPSNMSYVKETVDRLLKGYDIRLRPDFGGPPVDVGMRIDVASIDMVSEVNMDYTLT
MYFQQSWKDKRLSYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHP
DGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWNGGEGAVTGVNK
IELPQFSIVDYKMVSKKVEFTTGAYPRLSLSFRLKRNIGYFILQTYMPSTLITILSWVSF
WINYDASAARVALGITTVLTMTTISTHLRETLPKIPYVKAIDIYLMGCFVFVFLALLEYA
FVNYIFFGKGPQKKGASKQDQSANEKNKLEMNKVQVDAHGNILLSTLEIRNETSGSEVLT
SVSDPKATMYSYDSASIQYRKPLSSREAYGRALDRHGVPSKGRIRRRASQLKVKIPDLTD
VNSIDKWSRMFFPITFSLFNVVYWLYYVH

Sequence of entity 4 (E), FASTA

>9CXD_4 Gamma-aminobutyric acid receptor subunit gamma-2 (chains E)
QKSDDDYEDYASNKTWVLTPKVPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVN
SIGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKAD
AHWITTPNRMLRIWNDGRVLYTLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIV
YQWKRSSVEVGDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQT
YIPCTLIVVLSWVSFWINKDAVPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFV
SVCFIFVFSALVEYGTLHYFVSNRKPSKDKDKKKKNPLLRMFSFKAPTIDIRPRSATIQM
NNATHLQERDEEYGYECLDGKDCASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPT
AFCLFNLVYWVSYLYL

Sequence of entity 5 (I), FASTA

>9CXD_5 Kappa Fab_1F4 Light Chain (chains I)
NIVMTQSPKSMSMSVGERVTLSCKASEYVGTYVSWYQQKPEQSPKLLIYGASNRYTGVPD
RFTGSGSATDFTLTIGSVQAEDLADYHCGQSYSYPTFGAGTKLELKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 6 (J), FASTA

>9CXD_6 IgG2b Fab_1F4 Heavy Chain (chains J)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMYWVKQRPEQGLEWIGRIDPANGDTKY
DPKFQGKATITTDTFSNTAYLQLSSLTSEDTAVYYCARKGLRWAMDYWGQGTSVTVSTAK
TTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPN
LEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHR
EDYNSTIRVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPP
PAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMK
TSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK

Ligands and cofactors

ID	Name	Formula	Copies
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
PIO	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-d…	C25 H49 O19 P3	1

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…

Browse structure collections

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