6TWP | pdb_00006twp

Binding domain of BoNT/A5

• PDB DOI: https://doi.org/10.2210/pdb6TWP/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-01-13 Released: 2020-07-22 
• Deposition Author(s): Davies, J.R., Acharya, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.136 (DCC) 

Starting Model: experimental

Literature

High-resolution crystal structures of the botulinum neurotoxin binding domains from subtypes A5 and A6.

Davies, J.R., Britton, A., Liu, S.M., Acharya, K.R.

(2020) FEBS Open Bio 10: 1474-1481

• PubMed: 32654405 
• DOI: https://doi.org/10.1002/2211-5463.12931
• Primary Citation Related Structures: 
  6TWO, 6TWP


• PubMed Abstract: 
  

  Clostridium botulinum neurotoxins (BoNTs) cause flaccid paralysis through inhibition of acetylcholine release from motor neurons; however, at tiny doses, this property is exploited for use as a therapeutic. Each member of the BoNT family of proteins consists of three distinct domains: a binding domain that targets neuronal cell membranes (H _C ), a translocation domain (H _N ) and a catalytic domain (LC). Here, we present high-resolution crystal structures of the binding domains of BoNT subtypes/A5 (H _C /A5) and/A6 (H _C /A6). These structures show that the core fold identified in other subtypes is maintained, but with subtle differences at the expected receptor-binding sites.

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Organizational Affiliation: 
• Department of Biology and Biochemistry, Claverton Down, University of Bath, Bath, UK.
Department of Biochemistry and Biophysics, Stockholm University, Sweden.
Ipsen Bioinnovation Limited, Milton Park, Abingdon, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.76 kDa 
• Atom Count: 4,350 
• Modeled Residue Count: 415 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin A5	A [auth AAA]	433	Clostridium botulinum	Mutation(s): 0  Gene Names: bont/A5, boNT
UniProt
Find proteins for C7BEA8 (Clostridium botulinum) Explore C7BEA8  Go to UniProtKB:  C7BEA8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	A [auth AAA]	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.136 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.547	α = 90
b = 60.266	β = 90
c = 185.147	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Davies, J.R., Acharya, K.R.

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description