4TSO

Crystal structure of FraC with DHPC bound (crystal form I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    4TSL, 4TSN, 4TSO, 4TSP, 4TSQ, 4TSY, 3VWI, 3W9P

  • 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 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 ...

    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: 
    • Purification, cloning and characterization of fragaceatoxin C, a novel actinoporin from the sea anemone Actinia fragacea
      Bellomio, A., Morante, K., Barlic, A., Gutierrez-Aguirre, I., Viguera, A.R., Gonzalez-Manas, J.M.
      (2009) Toxicon 54: 869

    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 CA, B179Actinia fragaceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B9W5G6 (Actinia fragacea)
Explore B9W5G6 
Go to UniProtKB:  B9W5G6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HXG (Subject of Investigation/LOI)
Query on HXG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], J [auth B], K [auth B]1,2-dihexanoyl-sn-glycero-3-phosphocholine
C20 H41 N O8 P
DVZARZBAWHITHR-GOSISDBHSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], L [auth B], M [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.059α = 90
b = 131.059β = 90
c = 49.45γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Data collection, Derived calculations