1S3R

Crystal structure of the human-specific toxin intermedilysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin

Polekhina, G.Giddings, K.S.Tweten, R.K.Parker, M.W.

(2005) Proc.Natl.Acad.Sci.Usa 102: 600-605

  • DOI: 10.1073/pnas.0403229101

  • PubMed Abstract: 
  • The cholesterol-dependent cytolysins (CDCs), a superfamily of pore-forming toxins, are characterized by a conserved undecapeptide motif that is believed to be critical for membrane recognition by means of cholesterol. Intermedilysin (ILY), an unusual ...

    The cholesterol-dependent cytolysins (CDCs), a superfamily of pore-forming toxins, are characterized by a conserved undecapeptide motif that is believed to be critical for membrane recognition by means of cholesterol. Intermedilysin (ILY), an unusual member of the CDCs, exhibits specificity for human cells and contains nonconservative substitutions in the motif. We show that the cellular specificity of ILY is based on its ability to specifically bind to human cells and does not involve some other feature of the CDC mechanism. Furthermore, cellular recognition by ILY appears to be encoded in domain 4 alone but does not involve the variant undecapeptide of ILY. We show that the undecapeptide is involved in the prepore-to-pore conversion of ILY and so demonstrate a direct connection between the structure of the undecapeptide and the prepore-to-pore transition. We have determined the crystal structure of ILY, which, when compared to the known structure of a prototypical CDC, suggests that the basic aspects of its 3D structure are likely to be conserved in all CDCs.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of the human-specific toxin intermedilysin
      Polekhina, G.,Giddings, K.S.,Tweten, R.K.,Parker, M.W.
      () TO BE PUBLISHED --: --
    • Redefining cholesterol's role in the mechanism of the cholesterol-dependent cytolysins
      Giddings, K.S.,Johnson, A.E.,Tweten, R.K.
      (2003) Proc.Natl.Acad.Sci.USA 100: 11315


    Organizational Affiliation

    Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
intermedilysin
A, B
535Streptococcus intermediusGene Names: ily
Find proteins for Q9LCB8 (Streptococcus intermedius)
Go to UniProtKB:  Q9LCB8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.450α = 90.00
b = 173.640β = 90.00
c = 105.110γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance