5MK8

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.212
R-Value Work: 0.179
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.7717/peerj.4552
Primary Citation of 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.

Organizational Affiliation

Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9R540
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B]	I [auth A], J [auth A], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B]