5MK8 | pdb_00005mk8

Crystal structure of the receptor-binding domain of the FA hybrid Clostridium botulinum neurotoxin

• PDB DOI: https://doi.org/10.2210/pdb5MK8/pdb

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


• Deposited: 2016-12-02 Released: 2018-03-28 
• Deposition Author(s): Davies, J.R., Acharya, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

High resolution crystal structures of the receptor-binding domain ofClostridium botulinumneurotoxin serotypes A and FA.

Davies, J.R., Hackett, G.S., Liu, S.M., Acharya, K.R.

(2018) PeerJ 6: e4552-e4552

• PubMed: 29576992 
• DOI: https://doi.org/10.7717/peerj.4552
• Primary Citation Related Structures: 
  5MK6, 5MK7, 5MK8


• PubMed Abstract: 
  

  The binding specificity of botulinum neurotoxins (BoNTs) is primarily a consequence of their ability to bind to multiple receptors at the same time. BoNTs consist of three distinct domains, a metalloprotease light chain (LC), a translocation domain (H _N ) and a receptor-binding domain (H _C ). Here we report the crystal structure of H _C /FA, complementing an existing structure through the modelling of a previously unresolved loop which is important for receptor-binding. Our H _C /FA structure also contains a previously unidentified disulphide bond, which we have also observed in one of two crystal forms of H _C /A1. This may have implications for receptor-binding and future recombinant toxin production.

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Organizational Affiliation: 
• Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
Ipsen Bioinnovation Limited, Abingdon, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 102.56 kDa 
• Atom Count: 7,553 
• Modeled Residue Count: 841 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin FA binding domain	A, B	437	Clostridium botulinum	Mutation(s): 0
UniProt
Find proteins for Q9R540 (Clostridium botulinum) Explore Q9R540  Go to UniProtKB:  Q9R540

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	I [auth A], J [auth A], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.009	α = 90
b = 118.009	β = 90
c = 173.826	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Davies, J.R., Acharya, K.R.

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary