2VL8

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP, CASTANOSPERMINE AND CALCIUM ION

• PDB DOI: https://doi.org/10.2210/pdb2VL8/pdb

• Classification: TOXIN
• Organism(s): Paraclostridium sordellii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-01-09 Released: 2008-06-17 
• Deposition Author(s): Jank, T., Ziegler, M.O.P., Schulz, G.E., Aktories, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.255 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Literature

Inhibition of the Glucosyltransferase Activity of Clostridial Rho/Ras-Glucosylating Toxins by Castanospermine.

Jank, T., Ziegler, M.O.P., Schulz, G.E., Aktories, K.

(2008) FEBS Lett 582: 2277

• PubMed: 18505687 
• DOI: https://doi.org/10.1016/j.febslet.2008.05.025
• Primary Citation of Related Structures:  
  2VL8


• PubMed Abstract: 
  

  Castanospermine was identified as an inhibitor of the Rho/Ras-glucosylating Clostridium sordellii lethal toxin and Clostridium difficile toxin B. Microinjection of castanospermine into embryonic bovine lung cells prevented the cytotoxic effects of toxins. The crystal structure of the glucosyltransferase domain of C. sordellii lethal toxin in complex with castanospermine, UDP and a calcium ion was solved at a resolution of 2.3A. The inhibitor binds in a conformation that brings its four hydroxyl groups and its N-atom almost exactly in the positions of the four hydroxyls and of the ring oxygen of the glucosyl moiety of UDP-glucose, respectively.

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Organizational Affiliation: 

Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität, Albertstrasse 25, Freiburg, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 192.8 kDa 
• Atom Count: 13,720 
• Modelled Residue Count: 1,609 
• Deposited Residue Count: 1,638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOTOXIN L	A, B, C	546	Paraclostridium sordellii	Mutation(s): 2  EC: 3.4.22
UniProt
Find proteins for Q46342 (Paraclostridium sordellii) Explore Q46342  Go to UniProtKB:  Q46342

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	D [auth A], I [auth B], L [auth C]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
CTS	E [auth A], J [auth B], M [auth C]	CASTANOSPERMINE C8 H15 N O4 JDVVGAQPNNXQDW-TVNFTVLESA-N
CA	F [auth A], G [auth A], H [auth A], K [auth B], N [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UDP	PDBBind:  2VL8	IC50: 3.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.255 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.689	α = 90
b = 191.332	β = 90
c = 205.384	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Jank, T., Ziegler, M.O.P., Schulz, G.E., Aktories, K.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other