› 5tpb

X-ray diffraction
2.6Å resolution

Binding domain of BoNT/A complexed with ganglioside variant

Released:
DOI: 10.2210/pdb5tpb/pdb
PDB entry 5tpb coloured by chain, front view.
PDB entry 5tpb coloured by chain, side view.
PDB entry 5tpb coloured by chain, top view.
Source organism: Clostridium botulinum
Primary publication:
Glycans Confer Specificity to the Recognition of Ganglioside Receptors by Botulinum Neurotoxin A.
Hamark C, Berntsson RP, Masuyer G, Henriksson LM, Gustafsson R, Stenmark P, Widmalm G
J Am Chem Soc 139 218-230 (2017)
PMID: 27958736

Function and Biology Details

Reaction catalysed: 
Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevin (also known as neuronal vesicle-associated membrane protein, VAMP), synaptosome-associated protein of 25 kDa (SNAP25) or syntaxin. No detected action on small molecule substrates.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-144070 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Botulinum neurotoxin A heavy chain Chains: A, B
Molecule details ›
Chains: A, B
Length: 444 amino acids
Theoretical weight: 51.71 KDa
Source organism: Clostridium botulinum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DPI1 (Residues: 876-1296; Coverage: 33%)
Gene names: CBO0806, CLC_0862, bna, botA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NGA, GAL
Carbohydrate polymer
1 bound ligand:
Ligand SIA 1 x SIA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 65.515Å b: 104.33Å c: 69.406Å
α: 90° β: 115.97° γ: 90°
R-values:
R R work R free
0.223 0.222 0.24
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Botulinum and Tetanus Neurotoxins.
Dong et al. (2019)
9 more

1 mention without citation

High-resolution crystal structures of the botulinum neurotoxin binding domains from subtypes A5 and A6.
Davies et al. (2020)