7PBZ: A1b3 GABA-A receptor + GABA + Zn2+

a1b3 GABA-A receptor + GABA + Zn2+. Determined by electron microscopy at 2.79 Å resolution. Released 9 Feb 2022.

Method: Electron microscopy
Resolution: 2.79 Å
Organisms: Lama glama, Homo sapiens
Chains: 6
Atoms: 14,822
Mol. weight: 306.21 kDa
Ligands: NAG, UND, OCT, HEX
Released: 9 Feb 2022

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

Secondary structure: helices and β-sheets

7PBZ contains 65 α-helices and 73 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: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-22	9
α-helix	31	1
β-strand	39-54	16	3
β-strand	59-71	13	3
α-helix	73-75	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	175-178	4
β-strand	180-181	2	3
β-strand	191-203	13	4
β-strand	210-221	12	4
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-243	12
α-helix	252-276	25
α-helix	285-309	25
α-helix	315-414	29

Chain B: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	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	6
β-strand	101-106	6	5
β-strand	114-118	5	5
β-strand	123-135	13	5
α-helix	140-142	3
β-strand	147-156	10	6
β-strand	164-168	5	5
α-helix	171-173	3
β-strand	175-176	2	5
α-helix	178-180	3
β-strand	186-199	14	6
β-strand	204-216	13	6
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-242	16
α-helix	247-269	23
α-helix	280-307	28
α-helix	420-428	9
α-helix	431-445	15

Chain C: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-46	11	7
β-strand	50-51	2	7
β-strand	56-68	13	7
α-helix	70-72	3
β-strand	82-83	2	7
α-helix	85-90	6
β-strand	96-98	3	8
β-strand	101-106	6	7
β-strand	114-118	5	7
β-strand	123-135	13	7
α-helix	140-142	3
β-strand	147-156	10	8
β-strand	164-168	5	7
α-helix	171-173	3
β-strand	175-176	2	7
β-strand	186-199	14	8
β-strand	204-216	13	8
α-helix	221	1
α-helix	222-226	5
α-helix	227-241	15
α-helix	247-270	24
α-helix	280-307	28
α-helix	421-445	25

Chain D: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-49	11	11
β-strand	53-54	2	11
β-strand	59-71	13	11
α-helix	73-75	3
β-strand	83-86	4	11
α-helix	89-92	4
β-strand	99-101	3	12
β-strand	104-109	6	11
β-strand	117-122	6	11
β-strand	126-138	13	11
β-strand	150-159	10	12
β-strand	167-171	5	11
α-helix	176-178	3
β-strand	179-181	3	11
β-strand	191-204	14	12
β-strand	209-221	13	12
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	285-309	25
α-helix	315-416	31

Chain E: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	28	1
α-helix	35	1
β-strand	36-51	16	9
β-strand	56-68	13	9
α-helix	70-72	3
β-strand	81-83	3	9
α-helix	85-89	5
β-strand	96-98	3	10
β-strand	101-106	6	9
β-strand	114-118	5	9
β-strand	123-135	13	9
α-helix	140-142	3
β-strand	147-156	10	10
β-strand	164-168	5	9
α-helix	171-174	4
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	247-271	25
α-helix	280-307	28
α-helix	423-448	26

Chain F: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	406-413	8	1
β-strand	420-426	7	2
β-strand	433-439	7	2
β-strand	445-447	3	2
β-strand	455-460	6	1
β-strand	465-470	6	1
α-helix	475-477	3
β-strand	479-486	8	2
α-helix	496-498	3
β-strand	499-502	4	2
α-helix	503-505	3
β-strand	506-508	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Megabody 25	F	protein	522	Lama glama
Gamma-aminobutyric acid receptor subunit alpha-1	A	protein	368	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-3	B, C, E	protein	451	Homo sapiens	P28472 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-1	D	protein	411	Homo sapiens	P14867 (AlphaFold model)

Sequence of entity 1 (F), FASTA

>7PBZ_1 Megabody 25 (chains F)
QVQLQESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSR
LLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGY
AVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLS
IEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGHTFNYPI
MGWFRQAPGKEREFVGAISWSGGSTSYADSVKDRFTISRDNAKNTVYLEMNNLKPEDTAV
YYCAAKGRYSGGLYYPTNYDYWGQGTQVTVSSHHHHHHEPEA

Sequence of entity 2 (A), FASTA

>7PBZ_2 Gamma-aminobutyric acid receptor subunit alpha-1 (chains A)
QPSQDELKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYT
IDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRI
TEDGTLLYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVV
AEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILS
QVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSAL
IEFATVNYFTKSQPARAAKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQGTT
ESTQVAPA

Sequence of entity 3 (B, C, E), FASTA

>7PBZ_3 Gamma-aminobutyric acid receptor subunit beta-3 (chains B, C, E)
QSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLT
MYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHP
DGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVER
IELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSF
WINYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYA
FVNYIFFSQPAGTADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPK
LEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLT
GRAAAIDRWSRIVFPFTFSLFNLVYWLYYVN

Sequence of entity 4 (D), FASTA

>7PBZ_4 Gamma-aminobutyric acid receptor subunit alpha-1 (chains D)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPDYDIPTTENLYFQGTGQPSQDE
LKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFR
QSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTL
LYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVVVAEDGSR
LNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWL
NRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATV
NYFTKSQPARAAKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
UND	Undecane	C11 H24	2
OCT	N-octane	C8 H18	2
HEX	Hexane	C6 H14	4
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2
HSM	Histamine	C5 H9 N3	1
D10	Decane	C10 H22	3
ZN	Zinc ion	Zn	1

Primary citation

Mechanisms of inhibition and activation of extrasynaptic alpha beta GABA A receptors. Kasaragod, V.B., Mortensen, M., Hardwick, S.W. et al. Nature (2022) 602:529-533. DOI 10.1038/s41586-022-04402-z · 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…
7QNE 2.7 Å, Cryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex…

Browse structure collections

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