2QV3

Crystal Structure of the Helicobacter pylori Vacuolating Toxin p55 Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.401 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the Helicobacter pylori vacuolating toxin p55 domain

Gangwer, K.A.Mushrush, D.J.Stauff, D.L.Spiller, B.McClain, M.S.Cover, T.L.Lacy, D.B.

(2007) Proc.Natl.Acad.Sci.Usa 104: 16293-16298

  • DOI: 10.1073/pnas.0707447104

  • PubMed Abstract: 
  • Helicobacter pylori VacA, a pore-forming toxin secreted by an autotransporter pathway, causes multiple alterations in human cells, contributes to the pathogenesis of peptic ulcer disease and gastric cancer, and is a candidate antigen for inclusion in ...

    Helicobacter pylori VacA, a pore-forming toxin secreted by an autotransporter pathway, causes multiple alterations in human cells, contributes to the pathogenesis of peptic ulcer disease and gastric cancer, and is a candidate antigen for inclusion in an H. pylori vaccine. Here, we present a 2.4-A crystal structure of the VacA p55 domain, which has an important role in mediating VacA binding to host cells. The structure is predominantly a right-handed parallel beta-helix, a feature that is characteristic of autotransporter passenger domains but unique among known bacterial protein toxins. Notable features of VacA p55 include disruptions in beta-sheet contacts that result in five beta-helix subdomains and a C-terminal domain that contains a disulfide bond. Analysis of VacA protein sequences from unrelated H. pylori strains, including m1 and m2 forms of VacA, allows us to identify structural features of the VacA surface that may be important for interactions with host receptors. Docking of the p55 structure into a 19-A cryo-EM map of a VacA dodecamer allows us to propose a model for how VacA monomers assemble into oligomeric structures capable of membrane channel formation.


    Organizational Affiliation

    Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolating cytotoxin
A
457Helicobacter pyloriMutation(s): 0 
Gene Names: vacA
Find proteins for Q48245 (Helicobacter pylori)
Go to UniProtKB:  Q48245
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.401 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 56.606α = 90.00
b = 56.606β = 90.00
c = 256.895γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHARPphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data collection
DMphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-08-07 
  • Released Date: 2007-10-23 
  • Deposition Author(s): Gangwer, K.A.

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description