4TSO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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: 
    • 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

    Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fragaceatoxin C
A, B
179Actinia fragaceaMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
Protein: 
FraC eukaryotic pore-forming toxin from sea anemone
Find proteins for B9W5G6 (Actinia fragacea)
Go to UniProtKB:  B9W5G6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HXG
Query on HXG

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Download CCD File 
A, B
1,2-dihexanoyl-sn-glycero-3-phosphocholine
(4R,7R)-7-(hexanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphapentadecan-1-aminium 4-oxide
C20 H41 N O8 P
DVZARZBAWHITHR-GOSISDBHSA-O
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.059α = 90.00
b = 131.059β = 90.00
c = 49.450γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references