5IMY | pdb_00005imy

Trapped Toxin

• PDB DOI: https://doi.org/10.2210/pdb5IMY/pdb

• Classification: toxin/toxin receptor
• Organism(s): Gardnerella vaginalis, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMmpstruc


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.235 (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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 126.63 kDa 
• Atom Count: 8,802 
• Modeled Residue Count: 1,102 
• Deposited Residue Count: 1,136 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vaginolysin	A, D [auth B]	490	Gardnerella vaginalis	Mutation(s): 0  Gene Names: VLY, vly Membrane Entity: Yes
UniProt
Find proteins for B2YGA4 (Gardnerella vaginalis) Explore B2YGA4  Go to UniProtKB:  B2YGA4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CD59 glycoprotein	B [auth C], C [auth D]	78	Homo sapiens	Mutation(s): 0  Gene Names: CD59, MIC11, MIN1, MIN2, MIN3, MSK21 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P13987 (Homo sapiens) Explore P13987  Go to UniProtKB:  P13987
PHAROS:  P13987 GTEx:  ENSG00000085063

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.894	α = 90
b = 141.713	β = 90
c = 106.732	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Lawrence, S.L., 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: 2024-11-06
  Changes: Structure summary