5ETE

Structure of pathogen-related yeast protein, Pry1 in complex with a competitive inhibitor of cholesterol binding

• PDB DOI: https://doi.org/10.2210/pdb5ETE/pdb

• Classification: Sterol binding protein
• Organism(s): Saccharomyces cerevisiae YJM1434
• Expression System: Pichia
• Mutation(s): No 


• Deposited: 2015-11-17 Released: 2016-07-20 
• Deposition Author(s): Asojo, O.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.190 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein.

Darwiche, R., Kelleher, A., Hudspeth, E.M., Schneiter, R., Asojo, O.A.

(2016) Sci Rep 6: 28838-28838

• PubMed: 27344972 
• DOI: https://doi.org/10.1038/srep28838
• Primary Citation of Related Structures:  
  5ETE, 5JYS


• PubMed Abstract: 
  

  The production, crystal structure, and functional characterization of the C-terminal cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domain of pathogen-related yeast protein-1 (Pry1) from Saccharomyces cerevisiae is presented. The CAP domain of Pry1 (Pry1CAP) is functional in vivo as its expression restores cholesterol export to yeast mutants lacking endogenous Pry1 and Pry2. Recombinant Pry1CAP forms dimers in solution, is sufficient for in vitro cholesterol binding, and has comparable binding properties as full-length Pry1. Two crystal structures of Pry1CAP are reported, one with Mg(2+) coordinated to the conserved CAP tetrad (His208, Glu215, Glu233 and His250) in spacegroup I41 and the other without divalent cations in spacegroup P6122. The latter structure contains four 1,4-dioxane molecules from the crystallization solution, one of which sits in the cholesterol binding site. Both structures reveal that the divalent cation and cholesterol binding sites are connected upon dimerization, providing a structural basis for the observed Mg(2+)-dependent sterol binding by Pry1.

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Organizational Affiliation: 

Division of Biochemistry, Department of Biology, University of Fribourg Chemin du Musée 10 CH 1700 Fribourg Switzerland.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 16.26 kDa 
• Atom Count: 1,270 
• Modelled Residue Count: 142 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pry1p	A	149	Saccharomyces cerevisiae YJM1434	Mutation(s): 0  Gene Names: PRY1, H819_YJM1434J00135

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	B [auth A], C [auth A], D [auth A], E [auth A]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.190 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.74	α = 90
b = 124.74	β = 90
c = 59.06	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Asojo, O.A.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description