Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.77 kDa 
• Atom Count: 2097 
• Modelled Residue Count: 253 
• Deposited Residue Count: 262 
• Unique protein chains: 1

2F1N

Structure of CdtB, the biologically active subunit of Cytolethal Distending Toxin

• PDB DOI: 10.2210/pdb2F1N/pdb

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


• Deposited: 2005-11-14 Released: 2006-07-04 
• Deposition Author(s): Hontz, J.S., Yoder, M.D., Dreyfus, L.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Differences in Crystal and Solution Structures of the Cytolethal Distending Toxin B Subunit: RELEVANCE TO NUCLEAR TRANSLOCATION AND FUNCTIONAL ACTIVATION.

Hontz, J.S., Villar-Lecumberri, M.T., Potter, B.M., Yoder, M.D., Dreyfus, L.A., Laity, J.H.

(2006) J Biol Chem 281: 25365-25372

• PubMed: 16809347 
• DOI: 10.1074/jbc.M603727200
• Primary Citation of Related Structures:  
  2F1N


• PubMed Abstract: 
  

Cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells, which are mediated by the DNA-damaging CdtB subunit. Here we report the first x-ray structure of an isolated CdtB subunit (Escherichia coli-II CdtB, EcCdtB). In conjunction with previous structural and biochemical observations, active site structural comparisons between free and holotoxin-assembled CdtBs suggested that CDT intoxication is contingent upon holotoxin disassembly. Solution NMR structural and 15N relaxation studies of free EcCdtB revealed disorder in the interface with the CdtA and CdtC subunits (residues Gly233-Asp242). Residues Leu186-Thr209 of EcCdtB, which encompasses tandem arginine residues essential for nuclear translocation and intoxication, were also disordered in solution. In stark contrast, nearly identical well defined alpha-helix and beta-strand secondary structures were observed in this region of the free and holotoxin CdtB crystallographic models, suggesting that distinct changes in structural ordering characterize subunit disassembly and nuclear localization factor binding functions.

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Organizational Affiliation: 

Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri, Kansas City, Missouri 64110-2499, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytolethal distending toxin subunit B	A	262	Escherichia coli	Mutation(s): 0  Gene Names: cdtB EC: 3.1
UniProt
Find proteins for Q46669 (Escherichia coli) Explore Q46669  Go to UniProtKB:  Q46669

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.884	α = 90
b = 47.539	β = 90
c = 114.888	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-14 
• Released Date: 2006-07-04 
Deposition Author(s): Hontz, J.S., Yoder, M.D., Dreyfus, L.A.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description