4HSC | pdb_00004hsc

Crystal structure of a cholesterol dependent cytolysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.265 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.222 (Depositor) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration.

Feil, S.C.Ascher, D.B.Kuiper, M.J.Tweten, R.K.Parker, M.W.

(2014) J Mol Biology 426: 785-792

  • DOI: https://doi.org/10.1016/j.jmb.2013.11.020
  • Primary Citation Related Structures: 
    4HSC

  • PubMed Abstract: 

    Cholesterol-dependent cytolysins (CDCs) are a large family of bacterial toxins that exhibit a dependence on the presence of membrane cholesterol in forming large pores in cell membranes. Significant changes in the three-dimensional structure of these toxins are necessary to convert the soluble monomeric protein into a membrane pore. We have determined the crystal structure of the archetypical member of the CDC family, streptolysin O (SLO), a virulence factor from Streptococcus pyogenes. The overall fold is similar to previously reported CDC structures, although the C-terminal domain is in a different orientation with respect to the rest of the molecule. Surprisingly, a signature stretch of CDC sequence called the undecapeptide motif, a key region involved in membrane recognition, adopts a very different structure in SLO to that of the well-characterized CDC perfringolysin O (PFO), although the sequences in this region are identical. An analysis reveals that, in PFO, there are complementary interactions between the motif and the rest of domain 4 that are lost in SLO. Molecular dynamics simulations suggest that the loss of a salt bridge in SLO and a cation-pi interaction are determining factors in the extended conformation of the motif, which in turn appears to result in a greater flexibility of the neighboring L1 loop that houses a cholesterol-sensing motif. These differences may explain the differing abilities of SLO and PFO to efficiently penetrate target cell membranes in the first step of toxin insertion into the membrane.


  • Organizational Affiliation
    • ACRF Rational Drug Discovery Centre, Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.

Macromolecule Content 

  • Total Structure Weight: 63.72 kDa 
  • Atom Count: 3,842 
  • Modeled Residue Count: 469 
  • Deposited Residue Count: 571 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Streptolysin OA [auth X]571Streptococcus pyogenes SSI-1Mutation(s): 0 
Gene Names: sloSPs0132
EC: 3.2.2.5
Membrane Entity: Yes 
UniProt
Find proteins for P0DF97 (Streptococcus pyogenes serotype M3 (strain SSI-1))
Explore P0DF97 
Go to UniProtKB:  P0DF97
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DF97
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.265 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.222 (Depositor) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.208α = 90
b = 85.343β = 92.08
c = 81.223γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description