4OW6

Crystal structure of Diphtheria Toxin at acidic pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 

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This is version 1.3 of the entry. See complete history


Literature

Diphtheria toxin conformational switching at acidic pH.

Leka, O.Vallese, F.Pirazzini, M.Berto, P.Montecucco, C.Zanotti, G.

(2014) FEBS J 281: 2115-2122

  • DOI: https://doi.org/10.1111/febs.12783
  • Primary Citation of Related Structures:  
    4OW6

  • PubMed Abstract: 

    Diphtheria toxin (DT), the etiological agent of the homonymous disease, like other bacterial toxins, has to undergo a dramatic structural change in order to be internalized into the cytosol, where it finally performs its function. The molecular mechanism of toxin transit across the membrane is not well known, but the available experimental evidence indicates that one of the three domains of the toxin, called the central α-helical domain, inserts into the lipid bilayer, so favoring the translocation of the catalytic domain. This process is driven by the acidic pH of the endosomal lumen. Here, we describe the crystal structure of DT grown at acidic pH in the presence of bicelles. We were unable to freeze the moment of DT insertion into the lipid bilayer, but our crystal structure indicates that the low pH causes the unfolding of the TH2, TH3 and TH4 α-helices. This event gives rise to the exposure of a hydrophobic surface that includes the TH5 and TH8 α-helices, and the loop region connecting the TH8 and TH9 α-helices. Their exposure is probably favored by the presence of lipid bilayers in the crystallization solution, and they appear to be ready to insert into the membrane.


  • Organizational Affiliation

    Department of Biomedical Sciences, University of Padua, Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diphtheria toxin
A, B
535Corynebacterium diphtheriae C7 (beta)Mutation(s): 0 
EC: 2.4.2.36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.44α = 90
b = 141.28β = 90
c = 176.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary