5IMY image
Deposition Date 2016-03-07
Release Date 2016-08-24
Last Version Date 2024-11-06
Entry Detail
PDB ID:
5IMY
Title:
Trapped Toxin
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Vaginolysin
Gene (Uniprot):VLY
Chain IDs:A, D (auth: B)
Chain Length:490
Number of Molecules:2
Biological Source:Gardnerella vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CD59 glycoprotein
Gene (Uniprot):CD59
Chain IDs:B (auth: C), C (auth: D)
Chain Length:78
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.
Structure 24 1488 1498 (2016)
PMID: 27499440 DOI: 10.1016/j.str.2016.06.017

Abstact

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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Primary Citation of related structures