1SR4

Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Assembly and Function of a Bacterial Genotoxin

Nesic, D., Hsu, Y., Stebbins, C.E.

(2004) Nature 429: 429-433

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytolethal distending toxin subunit AA206[Haemophilus] ducreyiMutation(s): 0 
Gene Names: cdtA, HD0902
Membrane Entity: Yes 
UniProt
Find proteins for O06522 (Haemophilus ducreyi (strain 35000HP / ATCC 700724))
Explore O06522 
Go to UniProtKB:  O06522
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06522
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cytolethal distending toxin protein BB261[Haemophilus] ducreyiMutation(s): 0 
Gene Names: cdtB
Membrane Entity: Yes 
UniProt
Find proteins for O06523 (Haemophilus ducreyi)
Explore O06523 
Go to UniProtKB:  O06523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06523
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
cytolethal distending toxin protein CC166[Haemophilus] ducreyiMutation(s): 0 
Gene Names: cdtC
Membrane Entity: Yes 
UniProt
Find proteins for O06524 (Haemophilus ducreyi)
Explore O06524 
Go to UniProtKB:  O06524
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06524
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
E [auth A],
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth C],
Z [auth C]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
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 = 71.652α = 90
b = 75.653β = 90
c = 121.637γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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