4TSY

Crystal structure of FraC with lipids


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/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 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.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of the Basque Country, Lejona, Vizcaya 48940, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fragaceatoxin C
A, B, C, D
179Actinia fragaceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B9W5G6 (Actinia fragacea)
Explore B9W5G6 
Go to UniProtKB:  B9W5G6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9W5G6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HXJ
Query on HXJ

Download Ideal Coordinates CCD File 
DA [auth D]
E [auth A]
EA [auth D]
F [auth A]
FA [auth D]
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
N [auth B],
O [auth B],
P [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
2-[[(E,2S,3R)-2-(hexanoylamino)-3-oxidanyl-dec-4-enoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium
C21 H44 N2 O6 P
XVUOEYGVFVFEDQ-FGXJKGHSSA-O
HTO
Query on HTO

Download Ideal Coordinates CCD File 
M [auth A]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
G [auth A]
GA [auth D]
AA [auth C],
BA [auth C],
CA [auth C],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.337α = 90
b = 199.879β = 90
c = 120.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description