5IMY

Trapped Toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.

Lawrence, S.L.Gorman, M.A.Feil, S.C.Mulhern, T.D.Kuiper, M.J.Ratner, A.J.Tweten, R.K.Morton, C.J.Parker, M.W.

(2016) Structure 24: 1488-1498

  • DOI: 10.1016/j.str.2016.06.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cholesterol-dependent cytolysins (CDCs) are a family of pore-forming toxins that punch holes in the outer membrane of eukaryotic cells. Cholesterol serves as the receptor, but a subclass of CDCs first binds to human CD59. Here we describe the crystal ...

    Cholesterol-dependent cytolysins (CDCs) are a family of pore-forming toxins that punch holes in the outer membrane of eukaryotic cells. Cholesterol serves as the receptor, but a subclass of CDCs first binds to human CD59. Here we describe the crystal structures of vaginolysin and intermedilysin complexed to CD59. These studies, together with small-angle X-ray scattering, reveal that CD59 binds to each at different, though overlapping, sites, consistent with molecular dynamics simulations and binding studies. The CDC consensus undecapeptide motif, which for the CD59-responsive CDCs has a proline instead of a tryptophan in the motif, adopts a strikingly different conformation between the structures; our data suggest that the proline acts as a selectivity switch to ensure CD59-dependent CDCs bind their protein receptor first in preference to cholesterol. The structural data suggest a detailed model of how these water-soluble toxins assemble as prepores on the cell surface.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.,ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia.,Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville, VIC 3010, Australia.,ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: mparker@svi.edu.au.,Departments of Pediatrics and Microbiology, New York University School of Medicine, New York, NY 10016, USA.,Department of Microbiology and Immunology, University of Oklahoma, Health Sciences Center, Oklahoma City, OK 73104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vaginolysin
A, B
490Gardnerella vaginalisMutation(s): 0 
Gene Names: VLY (vly)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
VLYml Cholesterol-dependent cytolysin, CD-59 responsive, bound to CD59D22A
Find proteins for B2YGA4 (Gardnerella vaginalis)
Go to UniProtKB:  B2YGA4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CD59 glycoprotein
C, D
78Homo sapiensMutation(s): 0 
Gene Names: CD59 (MIC11, MIN1, MIN2, MIN3, MSK21)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
VLYml Cholesterol-dependent cytolysin, CD-59 responsive, bound to CD59D22A
Find proteins for P13987 (Homo sapiens)
Go to Gene View: CD59
Go to UniProtKB:  P13987
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.894α = 90.00
b = 141.713β = 90.00
c = 106.732γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references