Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 72.32 kDa 
• Atom Count: 5039 
• Residue Count: 579 
• Unique protein chains: 3

1SR4

Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin

• DOI: 10.2210/pdb1SR4/pdb

• Classification: TOXIN
• Organism(s): [Haemophilus] ducreyi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-22 Released: 2004-06-15 
• Deposition Author(s): Nesic, D., Hsu, Y., Stebbins, C.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Assembly and Function of a Bacterial Genotoxin

Nesic, D., Hsu, Y., Stebbins, C.E.

(2004) Nature 429: 429-433

• PubMed: 15164065 
• DOI: 10.1038/nature02532
• Primary Citation of Related Structures:  
  1SR4


• PubMed Abstract: 
  

The tripartite cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells. The subunits CdtA and CdtC associate with the nuclease CdtB to form a holotoxin that translocates CdtB into the host cell, where it acts as a genotoxin by creating DNA lesions. Here we show that the crystal structure of the holotoxin from Haemophilus ducreyi reveals that CDT consists of an enzyme of the DNase-I family, bound to two ricin-like lectin domains. CdtA, CdtB and CdtC form a ternary complex with three interdependent molecular interfaces, characterized by globular, as well as extensive non-globular, interactions. The lectin subunits form a deeply grooved, highly aromatic surface that we show to be critical for toxicity. The holotoxin possesses a steric block of the CdtB active site by means of a non-globular extension of the CdtC subunit, and we identify putative DNA binding residues in CdtB that are essential for toxin activity.

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Organizational Affiliation: 

Laboratory of Structural Microbiology, The Rockefeller University, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytolethal distending toxin subunit A	A	206	[Haemophilus] ducreyi	Mutation(s): 0  Gene Names: cdtA, HD0902
Find proteins for O06522 (Haemophilus ducreyi (strain 35000HP / ATCC 700724)) Explore O06522  Go to UniProtKB:  O06522

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cytolethal distending toxin protein B	B	261	[Haemophilus] ducreyi	Mutation(s): 0  Gene Names: cdtB
Find proteins for O06523 (Haemophilus ducreyi) Explore O06523  Go to UniProtKB:  O06523

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
cytolethal distending toxin protein C	C	166	[Haemophilus] ducreyi	Mutation(s): 0  Gene Names: cdtC
Find proteins for O06524 (Haemophilus ducreyi) Explore O06524  Go to UniProtKB:  O06524

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	A, B, C	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.652	α = 90
b = 75.653	β = 90
c = 121.637	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-22 
• Released Date: 2004-06-15 
Deposition Author(s): Nesic, D., Hsu, Y., Stebbins, C.E.

Revision History 

• Version 1.0: 2004-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance