3HVN

Crystal structure of cytotoxin protein suilysin from Streptococcus suis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of cytotoxin protein suilysin from Streptococcus suis.

Xu, L.Huang, B.Du, H.Zhang, X.C.Xu, J.Li, X.Rao, Z.

(2010) Protein Cell 1: 96-105

  • DOI: 10.1007/s13238-010-0012-3
  • Primary Citation of Related Structures:  
    3HVN

  • PubMed Abstract: 
  • Cholesterol-dependent cytolysins (CDC) are pore forming toxins. A prototype of the CDC family members is perfringolysin O (PFO), which directly binds to the cell membrane enriched in cholesterol, causing cell lysis. However, an exception of this general observation is intermedilysin (ILY) of Streptococcus intermedius, which requires human CD59 as a receptor in addition to cholesterol for its hemolytic activity ...

    Cholesterol-dependent cytolysins (CDC) are pore forming toxins. A prototype of the CDC family members is perfringolysin O (PFO), which directly binds to the cell membrane enriched in cholesterol, causing cell lysis. However, an exception of this general observation is intermedilysin (ILY) of Streptococcus intermedius, which requires human CD59 as a receptor in addition to cholesterol for its hemolytic activity. A possible explanation of this functional difference is the conformational variation between the C-terminal domains of the two toxins, particularly in the highly conserved undecapeptide termed tryptophan rich motif. Here, we present the crystal structure of suilysin, a CDC toxin from the infectious swine pathogen Streptococcus suis. Like PFO, suilysin does not require a host receptor for hemolytic activity; yet the crystal structure of suilysin exhibits a similar conformation in the tryptophan rich motif to ILY. This observation suggests that the current view of the structure-function relationship between CDC proteins and membrane association is far from complete.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemolysinA508Streptococcus suis 05ZYH33Mutation(s): 1 
Gene Names: slySSU05_1403
Membrane Entity: Yes 
UniProt
Find proteins for A4VW80 (Streptococcus suis (strain 05ZYH33))
Explore A4VW80 
Go to UniProtKB:  A4VW80
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFH (Subject of Investigation/LOI)
Query on CFH

Download Ideal Coordinates CCD File 
B [auth A]1,1,1,3,3,3-hexafluoropropan-2-ol
C3 H2 F6 O
BYEAHWXPCBROCE-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

Download Ideal Coordinates CCD File 
C [auth A]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.72α = 90
b = 95.72β = 90
c = 117.046γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2020-01-01
    Changes: Database references
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations