3W9P

Crystal structure of monomeric FraC (second crystal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for self-assembly of a cytolytic pore lined by protein and lipid

Tanaka, K.Caaveiro, J.M.M.Morante, K.Gonzalez-Manas, J.M.Tsumoto, K.

(2015) Nat Commun 6: 6337-6337

  • DOI: 10.1038/ncomms7337
  • Primary Citation of Related Structures:  
    3VWI, 3W9P, 4TSL, 4TSN, 4TSO, 4TSP, 4TSQ, 4TSY

  • PubMed Abstract: 
  • Pore-forming toxins (PFT) are water-soluble proteins that possess the remarkable ability to self-assemble on the membrane of target cells, where they form pores causing cell damage. Here, we elucidate the mechanism of action of the haemolytic protein ...

    Pore-forming toxins (PFT) are water-soluble proteins that possess the remarkable ability to self-assemble on the membrane of target cells, where they form pores causing cell damage. Here, we elucidate the mechanism of action of the haemolytic protein fragaceatoxin C (FraC), a α-barrel PFT, by determining the crystal structures of FraC at four different stages of the lytic mechanism, namely the water-soluble state, the monomeric lipid-bound form, an assembly intermediate and the fully assembled transmembrane pore. The structure of the transmembrane pore exhibits a unique architecture composed of both protein and lipids, with some of the lipids lining the pore wall, acting as assembly cofactors. The pore also exhibits lateral fenestrations that expose the hydrophobic core of the membrane to the aqueous environment. The incorporation of lipids from the target membrane within the structure of the pore provides a membrane-specific trigger for the activation of a haemolytic toxin.


    Related Citations: 
    • Structural insights into the oligomerization and architecture of eukaryotic membrane pore-forming toxins
      Mechaly, A.E., Bellomio, A., Gil-Carton, D., Morante, K., Valle, M., Gonzalez-Manas, J.M., Guerin, D.M.
      (2011) Structure 19: 181

    Organizational Affiliation

    1] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan [2] Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan [3] Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fragaceatoxin CAB180Actinia fragaceaMutation(s): 0 
Gene Names: FraC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
Protein: 
FraC toxin pore with bound lipids
Find proteins for B9W5G6 (Actinia fragacea)
Explore B9W5G6 
Go to UniProtKB:  B9W5G6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.98α = 90
b = 60.51β = 90
c = 80.84γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2016-08-03
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description