7QNE: GABA receptor subunit alpha-1

Cryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex with Ro15-4513 and megabody Mb38. Determined by electron microscopy at 2.7 Å resolution. Released 13 Apr 2022.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 15,302
Mol. weight: 290.77 kDa
Ligands: D10, PIO, EIE, NAG
Released: 13 Apr 2022

Explore 7QNE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QNE contains 64 α-helices and 79 β-strands across 6 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: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-54	16	1
β-strand	59-71	13	1
α-helix	73-75	3
β-strand	83	1	2
β-strand	86	1	1
α-helix	88-91	4
β-strand	99-101	3	3
β-strand	104	1	1
β-strand	108-109	2	1
β-strand	113	1	4
β-strand	117-121	5	1
β-strand	122	1	2
β-strand	126-138	13	1
α-helix	143-145	3
β-strand	150-159	10	3
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	3
β-strand	209-221	13	3
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	244-246	3
α-helix	252-274	23
α-helix	285-309	25
α-helix	316-318	3
α-helix	387-390	4
α-helix	391-417	27

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	35	1
β-strand	36-51	16	5
β-strand	56-68	13	5
α-helix	70-72	3
β-strand	81-83	3	5
α-helix	85-90	6
β-strand	96-98	3	4
β-strand	101-106	6	5
β-strand	114-118	5	5
β-strand	123-135	13	5
β-strand	147-156	10	4
β-strand	164-168	5	5
α-helix	171-173	3
β-strand	175-176	2	5
β-strand	186-199	14	4
β-strand	204-216	13	4
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-241	15
α-helix	247-271	25
α-helix	280-307	28
α-helix	420-446	27

Chain C: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
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	100-102	3
β-strand	111-113	3	7
β-strand	116-121	6	6
β-strand	129-134	6	6
β-strand	138-150	13	6
β-strand	162-171	10	7
β-strand	179-190	12	6
β-strand	201-214	14	7
β-strand	219-231	13	7
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-251	10
α-helix	253-256	4
α-helix	262-283	22
α-helix	295-321	27
α-helix	407-409	3
α-helix	410-434	25

Chain D: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-20	7
β-strand	39-54	16	8
β-strand	59-71	13	8
α-helix	73-75	3
β-strand	83-86	4	8
α-helix	88-91	4
β-strand	99-101	3	9
β-strand	104	1	8
β-strand	108-109	2	8
β-strand	117-122	6	8
β-strand	126-138	13	8
α-helix	143-145	3
β-strand	150-159	10	9
β-strand	167-171	5	8
α-helix	175-178	4
β-strand	179-181	3	8
β-strand	191-205	15	9
β-strand	208-221	14	9
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	244-246	3
α-helix	252-276	25
α-helix	285-308	24
α-helix	316-318	3
α-helix	387-390	4
α-helix	391-415	25

Chain E: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	10
β-strand	56-68	13	10
α-helix	70-72	3
β-strand	81-83	3	10
α-helix	85-90	6
β-strand	96-98	3	11
β-strand	101-106	6	10
β-strand	110	1	3
β-strand	114-118	5	10
β-strand	123-135	13	10
β-strand	147-156	10	11
β-strand	164-168	5	10
α-helix	171-173	3
β-strand	175-176	2	10
β-strand	186-199	14	11
β-strand	204-216	13	11
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-236	10
α-helix	237-241	5
α-helix	247-271	25
α-helix	280-307	28
α-helix	420-446	27

Chain G: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-13	3	13
β-strand	18-25	8	12
β-strand	33-39	7	3
β-strand	45-51	7	3
β-strand	56-59	4	3
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	87-89	3
β-strand	91-98	8	3
α-helix	107-109	3
β-strand	112-113	2	3
β-strand	114	1	12
β-strand	117-119	3	3
β-strand	120-122	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GABA(A) receptor subunit alpha-1	A, D	protein	456	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	B, E	protein	473	Homo sapiens	P28472 (AlphaFold model)
GABA(A) receptor subunit gamma-2	C	protein	495	Homo sapiens	P18507 (AlphaFold model)
Megabody Mb38	G	protein	123	Lama glama

Sequence of entity 1 (A, D), FASTA

>7QNE_1 GABA(A) receptor subunit alpha-1 (chains A, D)
MRKSPGLSDCLWAWILLLSTLTGRSYGQPSLQDELKDNTTVFTRILDRLLDGYDNRLRPG
LGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASK
IWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLYTMRLTVRAECPMHLEDFPMDAHAC
PLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVM
TTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISA
RNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGYAWDGKSVVPEKPKKVKDP
LIKKNNTYAPTATSYTPNLARGDPGLATIAKSATIEPKEVKPETKPPEPKKTFNSVSKID
RLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 2 (B, E), FASTA

>7QNE_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

>7QNE_3 GABA(A) receptor subunit gamma-2 (chains C)
MSSPNIWSTGSSVYSTPVFSQKMTVWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPK
VPEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQT
WYDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLY
TLRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQF
SFVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDA
VPARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFV
SNRKPSKDKDKKKKNPLLRMFSFKAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGK
DCASFFCCFEDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYLGGSGG
SGGSGKTETSQVAPA

Sequence of entity 4 (G), FASTA

>7QNE_4 Megabody Mb38 (chains G)
QVQLQESGGGLVQAGGSLRVSCAASGRTFTAYIMAWFRQAPGKEREFLAAMDQGRIQYYG
DSVRGRFTISRDYAKNSVDLQLDGLRPEDTAVYYCAAGAGFWGLRTASSYHYWGQGTQVT
VSS

Ligands and cofactors

ID	Name	Formula	Copies
D10	Decane	C10 H22	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	2
EIE	ethyl 8-[(azanylidene-$l^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{H}-…	C15 H14 N6 O3	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
OCT	N-octane	C8 H18	1

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

Primary citation

Differential assembly diversifies GABA A receptor structures and signalling. Sente, A., Desai, R., Naydenova, K. et al. Nature (2022) 604:190-194. DOI 10.1038/s41586-022-04517-3 · 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
9EQG 2.4 Å, CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA…
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…
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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