1S3R

Crystal structure of the human-specific toxin intermedilysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

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 U S A 102: 600-605

  • DOI: 10.1073/pnas.0403229101
  • Primary Citation of Related Structures:  
    1S3R

  • 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 member of the CDCs, exhibits specificity for human cells and contains nonconservative substitutions in the motif ...

    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 U S A 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
intermedilysinA, B535Streptococcus intermediusMutation(s): 0 
Gene Names: ily
Membrane Entity: Yes 
UniProt
Find proteins for Q9LCB8 (Streptococcus intermedius)
Explore Q9LCB8 
Go to UniProtKB:  Q9LCB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCB8
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.45α = 90
b = 173.64β = 90
c = 105.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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