5IMT

Toxin receptor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7001 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 

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
Intermedilysin
A
534Streptococcus intermediusMutation(s): 0 
Gene Names: ily
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
ILYml Cholesterol-dependent cytolysin, CD59-responsive
Find proteins for Q9LCB8 (Streptococcus intermedius)
Go to UniProtKB:  Q9LCB8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CD59 glycoprotein
D
77Homo 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: 
ILYml Cholesterol-dependent cytolysin, CD59-responsive
Find proteins for P13987 (Homo sapiens)
Go to Gene View: CD59
Go to UniProtKB:  P13987
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7001 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 93.730α = 90.00
b = 166.560β = 90.00
c = 118.250γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

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