5IMW | pdb_00005imw

Trapped Toxin

• PDB DOI: https://doi.org/10.2210/pdb5IMW/pdb

• Classification: TOXIN
• Organism(s): Streptococcus intermedius
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2016-03-07 Released: 2016-08-24 
• Deposition Author(s): Lawrence, S.L., Feil, S.C., Morton, C.J., Parker, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.295 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

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

• PubMed: 27499440 
• DOI: https://doi.org/10.1016/j.str.2016.06.017
• Primary Citation Related Structures: 
  5IMT, 5IMW, 5IMY


• 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 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.

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Organizational Affiliation: 
• 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.
Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville, VIC 3010, Australia.
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.
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103.77 kDa 
• Atom Count: 7,113 
• Modeled Residue Count: 918 
• Deposited Residue Count: 942 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermedilysin	A, B	471	Streptococcus intermedius	Mutation(s): 0  Gene Names: ily Membrane Entity: Yes
UniProt
Find proteins for Q9LCB8 (Streptococcus intermedius) Explore Q9LCB8  Go to UniProtKB:  Q9LCB8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.295 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.465	α = 90
b = 101.565	β = 90
c = 175.735	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Lawrence, S.L., Feil, S.C., Morton, C.J., Parker, M.W.

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary