9CXC: Gamma-aminobutyric acid receptor subunit beta-3

Native human GABAA receptor of beta3-alpha1-gamma2-beta2-alpha2 assembly. Determined by electron microscopy at 3.3 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Mus musculus
Chains: 7
Atoms: 14,577
Mol. weight: 334.61 kDa
Ligands: NAG, PIO, ABU
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

9CXC contains 49 α-helices and 109 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	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	1	1
α-helix	85-89	5
β-strand	96-98	3	2
β-strand	101	1	1
β-strand	105-106	2	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
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	219-221	3
α-helix	222-226	5
α-helix	227-229	3
α-helix	232-236	5
α-helix	237-240	4
α-helix	247-268	22
α-helix	280-307	28
α-helix	421-445	25

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-54	16	3
β-strand	59-71	13	3
β-strand	83-86	4	3
α-helix	88-93	6
β-strand	99-101	3	4
β-strand	104	1	3
β-strand	108-109	2	3
β-strand	117-122	6	3
β-strand	126-138	13	3
β-strand	150-159	10	4
β-strand	167-171	5	3
α-helix	175-177	3
β-strand	179-181	3	3
β-strand	193-204	12	4
β-strand	209-220	12	4
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-242	11
α-helix	243-246	4
α-helix	252-274	23
α-helix	285-309	25
α-helix	391-413	23

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	50	1
β-strand	51-66	16	5
β-strand	71-83	13	5
α-helix	85-87	3
β-strand	96-98	3	5
α-helix	100-102	3
β-strand	111-113	3	6
β-strand	116-121	6	5
β-strand	129-133	5	5
β-strand	138-150	13	5
β-strand	162-171	10	6
β-strand	179-189	11	5
β-strand	202-215	14	6
β-strand	218-230	13	6

Chain D: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-40	5	7
β-strand	43	1	8
β-strand	44-51	8	9
β-strand	56-61	6	9
β-strand	64	1	10
β-strand	65-66	2	7
β-strand	67-68	2	11
β-strand	81-83	3	11
α-helix	85-89	5
β-strand	96-98	3	12
β-strand	101-106	6	9
β-strand	114-115	2	10
β-strand	116-118	3	11
β-strand	123-124	2	11
β-strand	127-128	2	10
β-strand	130-135	6	9
β-strand	147-156	10	12
β-strand	164-168	5	7
α-helix	171-173	3
β-strand	176	1	8
β-strand	186-200	15	12
β-strand	203-216	14	12
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-241	15
α-helix	247-266	20
α-helix	269-271	3
α-helix	280-306	27
α-helix	462-485	24

Chain E: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
β-strand	38-43	6	13
β-strand	44-46	3	14
β-strand	48-49	2	15
β-strand	58	1	16
β-strand	61-63	3	15
β-strand	66-68	3	13
β-strand	70	1	17
β-strand	82-85	4	13
α-helix	88-90	3
β-strand	98-100	3	18
β-strand	103	1	19
β-strand	116-121	6	13
β-strand	125	1	17
β-strand	128-130	3	13
β-strand	132-134	3	15
β-strand	136	1	19
β-strand	137	1	16
α-helix	142-144	3
β-strand	151-158	8	18
β-strand	166-170	5	13
β-strand	178-180	3	14
β-strand	185	1	15
β-strand	190-204	15	18
β-strand	207-220	14	18
α-helix	223-225	3
α-helix	226-230	5
α-helix	231-240	10
α-helix	241-245	5
α-helix	251-272	22
α-helix	286-308	23
α-helix	388-411	24

Chain K: 0 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	20
β-strand	10-12	3	21
β-strand	18	1	22
β-strand	21-25	5	20
β-strand	34-39	6	23
β-strand	45-52	8	23
β-strand	57-60	4	23
β-strand	68	1	22
β-strand	71-73	3	20
β-strand	78-80	3	20
β-strand	83	1	22
β-strand	93-98	6	23
β-strand	108	1	23
β-strand	112-113	2	23
β-strand	114-116	3	21

Chain L: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	24
β-strand	10-12	3	25
β-strand	19-20	2	26
β-strand	23-25	3	24
β-strand	35-38	4	27
β-strand	45-48	4	27
β-strand	54	1	27
α-helix	55	1
β-strand	62-65	4	26
β-strand	70-71	2	24
β-strand	72-75	4	26
β-strand	85-88	4	27
β-strand	89	1	28
β-strand	97	1	28
β-strand	101	1	27
β-strand	102-104	3	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit beta-3	A	protein	448	Homo sapiens	P28472 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-1	B	protein	429	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	C	protein	436	Homo sapiens	P18507 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-2	D	protein	488	Homo sapiens	P47870 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-2	E	protein	423	Homo sapiens	P47869
IgG2b Fab_1F4 Heavy Chain	K	protein	454	Mus musculus
Kappa Fab_1F4 Light Chain	L	protein	213	Mus musculus

Sequence of entity 1 (A), FASTA

>9CXC_1 Gamma-aminobutyric acid receptor subunit beta-3 (chains A)
QSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLT
MYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHP
DGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVER
IELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSF
WINYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYA
FVNYIFFGRGPQRQKKLAEKTAKAKNDRSKSESNRVDAHGNILLTSLEVHNEMNEVSGGI
GDTRNSAISFDNSGIQYRKQSMPREGHGRFLGDRSLPHKKTHLRRRSSQLKIKIPDLTDV
NAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 2 (B), FASTA

>9CXC_2 Gamma-aminobutyric acid receptor subunit alpha-1 (chains B)
QPSLQDELKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEY
TIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLR
ITEDGTLLYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVV
VAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVIL
SQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSA
LIEFATVNYFTKRGYAWDGKSVVPEKPKKVKDPLIKKNNTYAPTATSYTPNLARGDPGLA
TIAKSATIEPKEVKPETKPPEPKKTFNSVSKIDRLSRIAFPLLFGIFNLVYWATYLNREP
QLKAPTPHQ

Sequence of entity 3 (C), FASTA

>9CXC_3 Gamma-aminobutyric acid receptor subunit gamma-2 (chains C)
QKSDDDYEDYASNKTWVLTPKVPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVN
SIGPVNAINMEYTIDIFFAQTWYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKAD
AHWITTPNRMLRIWNDGRVLYTLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIV
YQWKRSSVEVGDTRSWRLYQFSFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQT
YIPCTLIVVLSWVSFWINKDAVPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFV
SVCFIFVFSALVEYGTLHYFVSNRKPSKDKDKKKKNPLLRMFSFKAPTIDIRPRSATIQM
NNATHLQERDEEYGYECLDGKDCASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPT
AFCLFNLVYWVSYLYL

Sequence of entity 4 (D), FASTA

>9CXC_4 Gamma-aminobutyric acid receptor subunit beta-2 (chains D)
QSVNDPSNMSLVKETVDRLLKGYDIRLRPDFGGPPVAVGMNIDIASIDMVSEVNMDYTLT
MYFQQAWRDKRLSYNVIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHP
DGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGDDNAVTGVTK
IELPQFSIVDYKLITKKVVFSTGSYPRLSLSFKLKRNIGYFILQTYMPSILITILSWVSF
WINYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFMALLEYA
LVNYIFFGRGPQRQKKAAEKAASANNEKMRLDVNKIFYKDIKQNGTQYRSLWDPTGNLSP
TRRTTNYDFSLYTMDPHENILLSTLEIKNEMATSEAVMGLGDPRSTMLAYDASSIQYRKA
GLPRHSFGRNALERHVAQKKSRLRRRASQLKITIPDLTDVNAIDRWSRIFFPVVFSFFNI
VYWLYYVN

Sequence of entity 5 (E), FASTA

>9CXC_5 Gamma-aminobutyric acid receptor subunit alpha-2 (chains E)
NIQEDEAKNNITIFTRILDRLLDGYDNRLRPGLGDSITEVFTNIYVTSFGPVSDTDMEYT
IDVFFRQKWKDERLKFKGPMNILRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRI
QDDGTLLYTMRLTVQAECPMHLEDFPMDAHSCPLKFGSYAYTTSEVTYIWTYNASDSVQV
APDGSRLNQYDLLGQSIGKETIKSSTGEYTVMTAHFHLKRKIGYFVIQTYLPCIMTVILS
QVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSAL
IEFATVNYFTKRGWAWDGKSVVNDKKKEKASVMIQNNAYAVAVANYAPNLSKDPVLSTIS
KSATTPEPNKKPENKPAEAKKTFNSVSKIDRMSRIVFPVLFGTFNLVYWATYLNREPVLG
VSP

Sequence of entity 6 (K), FASTA

>9CXC_6 IgG2b Fab_1F4 Heavy Chain (chains K)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMYWVKQRPEQGLEWIGRIDPANGDTKY
DPKFQGKATITTDTFSNTAYLQLSSLTSEDTAVYYCARKGLRWAMDYWGQGTSVTVSTAK
TTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPN
LEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHR
EDYNSTIRVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPP
PAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMK
TSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK

Sequence of entity 7 (L), FASTA

>9CXC_7 Kappa Fab_1F4 Light Chain (chains L)
NIVMTQSPKSMSMSVGERVTLSCKASEYVGTYVSWYQQKPEQSPKLLIYGASNRYTGVPD
RFTGSGSATDFTLTIGSVQAEDLADYHCGQSYSYPTFGAGTKLELKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
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 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…

Browse structure collections

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