3A57

Crystal structure of Thermostable Direct Hemolysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin

Yanagihara, I.Nakahira, K.Yamane, T.Kaieda, S.Mayanagi, K.Hamada, D.Fukui, T.Ohnishi, K.Kajiyama, S.Shimizu, T.Sato, M.Ikegami, T.Ikeguchi, M.Honda, T.Hashimoto, H.

(2010) J Biol Chem 285: 16267-16274

  • DOI: https://doi.org/10.1074/jbc.M109.074526
  • Primary Citation of Related Structures:  
    3A57

  • PubMed Abstract: 

    Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 A resolution. The TDH tetramer forms a central pore with dimensions of 23 A in diameter and approximately 50 A in depth. Pi-cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin.


  • Organizational Affiliation

    Department of Developmental Medicine, Research Institute, Osaka Medical Center for Maternal and Child Health, Izumi City, Osaka 594-1101, Japan. itaruy@mch.pref.osaka.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermostable direct hemolysin 2165Vibrio parahaemolyticusMutation(s): 0 
Gene Names: tdh
UniProt
Find proteins for P19250 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore P19250 
Go to UniProtKB:  P19250
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19250
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.066α = 90
b = 63.066β = 90
c = 83.045γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary