3A57 | pdb_00003a57

Crystal structure of Thermostable Direct Hemolysin

• PDB DOI: https://doi.org/10.2210/pdb3A57/pdb

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


• Deposited: 2009-08-03 Released: 2010-03-31 
• Deposition Author(s): Hashimoto, H., Yanagihara, I., Nakahira, K., Hamada, D., Ikegami, T., Mayanagi, K., Kaieda, S., Fukui, T., Ohnishi, K., Kajiyama, S., Yamane, T., Ikeguchi, M., Honda, T., Shimizu, T., Sato, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.170 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

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 Biological Chem 285: 16267-16274

• PubMed: 20335168 
• DOI: https://doi.org/10.1074/jbc.M109.074526
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Developmental Medicine, Research Institute, Osaka Medical Center for Maternal and Child Health, Izumi City, Osaka 594-1101, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.66 kDa 
• Atom Count: 1,457 
• Modeled Residue Count: 154 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermostable direct hemolysin 2	A	165	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: tdh
UniProt
Find proteins for P19250 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore P19250  Go to UniProtKB:  P19250

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.170 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.066	α = 90
b = 63.066	β = 90
c = 83.045	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Hashimoto, H., Yanagihara, I., Nakahira, K., Hamada, D., Ikegami, T., Mayanagi, K., Kaieda, S., Fukui, T., Ohnishi, K., Kajiyama, S., Yamane, T., Ikeguchi, M., Honda, T., Shimizu, T., Sato, M.

Revision History  

• 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