8RVG: Binding domain of BoNT/A mutant Y1117V

Name: PDB 8RVG: Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a ganglioside receptor
Published: 2025-02-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a ganglioside receptor. Determined by X-ray diffraction at 1.9 Å resolution. Released 12 Feb 2025.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 7,268
Mol. weight: 104.97 kDa
Released: 12 Feb 2025

Explore 8RVG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RVG contains 16 α-helices and 88 β-strands across 2 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: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	877-880	4	1
β-strand	881-884	4	2
β-strand	887-890	4	2
β-strand	897-900	4	3
β-strand	904-906	3	1
β-strand	914-917	4	1
β-strand	924-927	4	3
α-helix	930-932	3
β-strand	935-936	2	4
β-strand	941-948	8	1
α-helix	950-952	3
α-helix	955-957	3
β-strand	962-969	8	3
β-strand	972-979	8	3
β-strand	982-988	7	3
β-strand	994-1000	7	3
β-strand	1004	1	5
β-strand	1015-1021	7	1
β-strand	1026-1031	6	1
β-strand	1034-1040	7	1
β-strand	1047-1048	2	4
β-strand	1052-1058	7	3
β-strand	1066-1075	10	1
α-helix	1081-1091	11
β-strand	1096	1	6
β-strand	1098	1	7
β-strand	1104	1	7
α-helix	1105	1
β-strand	1106	1	8
β-strand	1111-1115	5	9
β-strand	1122-1125	4	9
β-strand	1134-1137	4	9
β-strand	1142-1145	4	5
β-strand	1149-1152	4	5
β-strand	1160-1164	5	9
β-strand	1173	1	8
β-strand	1175	1	6
β-strand	1179-1185	7	9
β-strand	1190-1194	5	9
β-strand	1195	1	10
β-strand	1204-1205	2	9
β-strand	1207-1209	3	9
α-helix	1211-1213	3
β-strand	1218	1	10
β-strand	1220-1226	7	9
β-strand	1234-1240	7	9
β-strand	1246-1255	10	9
β-strand	1258-1264	7	9
α-helix	1265-1268	4
β-strand	1282-1285	4	9
α-helix	1293-1295	3

Chain B: 8 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	877-880	4	11
β-strand	881-884	4	12
β-strand	887-890	4	12
β-strand	897-900	4	13
β-strand	904-906	3	11
β-strand	914-917	4	11
β-strand	924-927	4	13
α-helix	930-932	3
β-strand	935-936	2	14
β-strand	941-948	8	11
α-helix	950-952	3
α-helix	955-957	3
β-strand	962-969	8	13
β-strand	972-979	8	13
β-strand	982-988	7	13
β-strand	994-1000	7	13
β-strand	1004	1	15
β-strand	1015-1021	7	11
β-strand	1026-1031	6	11
β-strand	1034-1040	7	11
β-strand	1047-1048	2	14
β-strand	1052-1058	7	13
β-strand	1066-1075	10	11
α-helix	1081-1091	11
β-strand	1096	1	16
β-strand	1098	1	17
β-strand	1104	1	17
α-helix	1105	1
β-strand	1106	1	18
β-strand	1111	1	19
β-strand	1112-1115	4	20
β-strand	1122-1125	4	19
β-strand	1134-1137	4	19
β-strand	1142-1145	4	15
β-strand	1149-1152	4	15
β-strand	1159-1164	6	19
β-strand	1173	1	18
β-strand	1175	1	16
β-strand	1179-1186	8	19
β-strand	1189-1194	6	19
β-strand	1195	1	21
β-strand	1204-1205	2	19
β-strand	1207-1209	3	19
α-helix	1211-1213	3
β-strand	1218	1	21
β-strand	1220-1224	5	19
β-strand	1235	1	20
β-strand	1236-1240	5	19
β-strand	1246-1255	10	19
β-strand	1258-1264	7	19
α-helix	1265-1269	5
β-strand	1282-1285	4	20
α-helix	1293-1295	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin A heavy chain	A, B	protein	444	Clostridium botulinum	P0DPI0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8RVG_1 Botulinum neurotoxin A heavy chain (chains A, B)
MGSSHHHHHHSSGLVPRGSHMDTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQ
IQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSG
WKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYING
RLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSN
SGILKDFWGDYLQYDKPYYMLNLVDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSS
LYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPD
VGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIER
SSRTLGCSWEFIPVDDGWGERPLQ

Primary citation

Botulinum neurotoxin A mutants with enhanced ganglioside binding show improved potency and altered ganglioside selectivity. Masuyer, G., Rummel, A., Stenmark, P. Commun Chem (2025) 8:171-171. DOI 10.1038/s42004-025-01569-0 · PubMed

Other PDB entries of the same protein (UniProt P0DPI0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RVI 1.6 Å, Structure of the binding domain of BoNT/A mutant H1253K in complex with the GM1a…
6XCF 1.68 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
6XCB 1.74 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
8RVH 1.8 Å, Structure of the binding domain of BoNT/A mutant Y1117V/H1253K in complex with the GD1a…
6XCC 1.9 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
6XCD 1.92 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
2IMA 1.94 Å, Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited by…
2ISG 2.0 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form B
2ISH 2.0 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form C
2ISE 2.2 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form A
7KYF 2.33 Å, Botulism Neurooxin Light Chain A app form
6XCE 2.5 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…

Browse structure collections

About this viewer

MolViewer shows 8RVG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.