9EQG: Human full-length alpha1beta3gamma2L GABA(A)R

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA and puerarin. Determined by electron microscopy at 2.4 Å resolution. Released 18 Sept 2024.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 5
Atoms: 15,459
Mol. weight: 286.64 kDa
Ligands: R16, PLM, PX2, HEX
Released: 18 Sept 2024

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

Secondary structure: helices and β-sheets

9EQG contains 68 α-helices and 68 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: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
β-strand	39-54	16	1
β-strand	59-71	13	1
α-helix	73-75	3
β-strand	83-86	4	1
α-helix	88-93	6
β-strand	99-101	3	2
β-strand	104	1	1
β-strand	108-109	2	1
β-strand	113	1	3
β-strand	117-122	6	1
β-strand	126-138	13	1
β-strand	150-159	10	2
β-strand	167-171	5	1
α-helix	175-178	4
β-strand	179-181	3	1
β-strand	186	1	1
β-strand	191-204	14	2
β-strand	209-221	13	2
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	244-246	3
α-helix	252-272	21
α-helix	285-309	25
α-helix	316-318	3
α-helix	387-390	4
α-helix	391-416	26

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	4
β-strand	56-68	13	4
α-helix	70-72	3
β-strand	82-83	2	4
α-helix	85-90	6
β-strand	96-97	2	3
β-strand	101-106	6	4
β-strand	110	1	5
β-strand	114-118	5	4
β-strand	123-135	13	4
β-strand	147-156	10	3
β-strand	164-168	5	4
α-helix	171-174	4
β-strand	175-176	2	4
β-strand	186-200	15	3
β-strand	203-216	14	3
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-241	5
α-helix	247-269	23
α-helix	280-307	28
α-helix	310-316	7
α-helix	420-446	27

Chain C: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	50	1
β-strand	51-66	16	6
β-strand	71-83	13	6
α-helix	85-87	3
β-strand	95-98	4	6
α-helix	100-104	5
β-strand	111-113	3	5
β-strand	116-121	6	6
β-strand	129-134	6	6
β-strand	138-150	13	6
β-strand	162-171	10	5
β-strand	179-182	4	6
β-strand	188-190	3	6
α-helix	193-195	3
β-strand	201-215	15	5
β-strand	218-231	14	5
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-252	11
α-helix	253-256	4
α-helix	262-283	22
α-helix	295-318	24
α-helix	319-323	5
α-helix	410-430	21
α-helix	431-435	5

Chain D: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
α-helix	38	1
β-strand	39-54	16	7
β-strand	59-71	13	7
α-helix	73-75	3
β-strand	83-86	4	7
α-helix	88-93	6
β-strand	99-101	3	8
β-strand	104	1	7
β-strand	108-109	2	7
β-strand	117-122	6	7
β-strand	126-138	13	7
β-strand	150-159	10	8
β-strand	167-171	5	7
α-helix	175-178	4
β-strand	179-181	3	7
β-strand	186	1	7
β-strand	191-204	14	8
β-strand	209-221	13	8
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	244-246	3
α-helix	252-273	22
α-helix	285-309	25
α-helix	322-324	3
α-helix	387-390	4
α-helix	391-417	27

Chain E: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-47	12	9
β-strand	51	1	9
β-strand	56-68	13	9
α-helix	70-72	3
β-strand	81-83	3	9
α-helix	85-90	6
β-strand	96-98	3	10
β-strand	101-106	6	9
β-strand	110	1	2
β-strand	114-118	5	9
β-strand	123-135	13	9
β-strand	147-156	10	10
β-strand	164-168	5	9
α-helix	171-173	3
β-strand	175-176	2	9
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	237-241	5
α-helix	247-269	23
α-helix	278-279	2
α-helix	280-307	28
α-helix	310-316	7
α-helix	420-446	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit alpha-1	A, D	protein	464	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	B, E	protein	473	Homo sapiens	P28472 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	C	protein	495	Homo sapiens	P18507 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9EQG_1 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, D)
MKKSPGLSDYLWAWTLFLSTLTGRSYGDYKDDDDKQPSLQDELKDNTTVFTRILDRLLDG
YDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLR
LNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLYTMRLTVRAECPMHLED
FPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQS
STGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLT
MTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVPE
KPKKVKDPLIKKNNTYAPTATSYTPNLARGDPGLATIAKSATIEPKEVKPETKPPEPKKT
FNSVSKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 2 (B, E), FASTA

>9EQG_2 Gamma-aminobutyric acid receptor subunit beta-3 (chains B, E)
MWGLAGGRLFGIFSAPVLVAVVCCAQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP
VCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPD
TYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIE
SYGYTTDDIEFYWRGGDKAVTGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLK
RNIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLTMTTINTHLRETLPKI
PYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFGRGPQRQKKLAEKTAKAKNDRSKSESNR
VDAHGNILLTSLEVHNEMNEVSGGIGDTRNSAISFDNSGIQYRKQSMPREGHGRFLGDRS
LPHKKTHLRRRSSQLKIKIPDLTDVNAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 3 (C), FASTA

>9EQG_3 Gamma-aminobutyric acid receptor subunit gamma-2 (chains C)
MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK
VPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQT
WYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLY
TLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQF
SFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDA
VPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFV
SNRKPSKDKDKKKKNPLLRMFSFKAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGK
DCASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYLGGSGG
SGGSGKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
R16	Hexadecane	C16 H34	5
PLM	Palmitic acid	C16 H32 O2	3
PX2	1,2-dilauroyl-sn-glycero-3-phosphate	C27 H52 O8 P	1
HEX	Hexane	C6 H14	10
D10	Decane	C10 H22	11
PGW	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexade…	C40 H77 O10 P	2
A1H6W	Puerarin	C21 H20 O9	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
PT5	[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4…	C47 H85 O19 P3	2

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

Primary citation

A brain-to-gut signal controls intestinal fat absorption. Lyu, Q., Xue, W., Liu, R. et al. Nature (2024) 634:936-943. DOI 10.1038/s41586-024-07929-5 · PubMed

Other PDB entries of the same protein (UniProt P14867 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RGD 2.0 Å, CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
9FAS 2.5 Å, CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with…
9FFU 2.5 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…
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
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…
9FAK 2.6 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with…
9FGG 2.6 Å, Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in Saposin A…
8SGO 2.65 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus pregnenolone…
7QNE 2.7 Å, Cryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex…
9FG7 2.7 Å, Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in complex with…

Browse structure collections

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