› 3rmy

X-ray diffraction
2.3Å resolution

Crystal structure of HCR/D W1238A mutant

Released:
DOI: 10.2210/pdb3rmy/pdb
PDB entry 3rmy coloured by chain, front view.
PDB entry 3rmy coloured by chain, side view.
PDB entry 3rmy coloured by chain, top view.
Source organism: Clostridium botulinum
Primary publication:
Novel ganglioside-mediated entry of botulinum neurotoxin serotype D into neurons.
Kroken AR, Karalewitz AP, Fu Z, Kim JJ, Barbieri JT
J Biol Chem 286 26828-37 (2011)
PMID: 21632541

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-148553 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Botulinum neurotoxin D heavy chain Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 415 amino acids
Theoretical weight: 48.12 KDa
Source organism: Clostridium botulinum
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P19321 (Residues: 862-1276; Coverage: 33%)
Gene name: botD
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 94.519Å b: 115.623Å c: 107.179Å
α: 90° β: 91.9° γ: 90°
R-values:
R R work R free
0.232 0.232 0.269
Expression system: Escherichia coli BL21

Quick links

Citations

10 review citations

Botulinum Neurotoxins: Biology, Pharmacology, and Toxicology.
Pirazzini et al. (2017)
9 more