4FES

Structure of OSH4 in complex with cholesterol analogs

• PDB DOI: https://doi.org/10.2210/pdb4FES/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-30 Released: 2013-06-12 
• Deposition Author(s): Koag, M.C., Monzingo, A.F., Cheun, Y., Lee, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.266 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Synthesis and structure of 16,22-diketocholesterol bound to oxysterol-binding protein Osh4.

Koag, M.C., Cheun, Y., Kou, Y., Ouzon-Shubeita, H., Min, K., Monzingo, A.F., Lee, S.

(2013) Steroids 78: 938-944

• PubMed: 23756172 
• DOI: https://doi.org/10.1016/j.steroids.2013.05.016
• Primary Citation of Related Structures:  
  4F4B, 4FES


• PubMed Abstract: 
  

  We have synthesized 16,22-diketocholesterol, a novel ligand for oxysterol-binding protein Osh4, and determined X-ray structure of the diketocholesterol in complex with Osh4. The X-ray structure shows that α7 helix of Osh4 assumes open conformation while the rest of Osh4, closed conformation, implying this diketocholesterol-bound Osh4 structure may represent a structural intermediate between the two conformations.

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Organizational Affiliation: 

Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA.

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: 100.4 kDa 
• Atom Count: 7,159 
• Modelled Residue Count: 856 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein KES1	A, B	436	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: KES1, OSH4, YPL145C, LPI3C, P2614
UniProt
Find proteins for P35844 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35844  Go to UniProtKB:  P35844

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0T9	C [auth A], D [auth B]	(3S,8S,9S,10R,13S,14S,17R)-3-hydroxy-10,13-dimethyl-17-[(2S,6S)-6-methyl-3-oxooctan-2-yl]-1,2,3,4,7,8,9,10,11,12,13,14,15,17-tetradecahydro-16H-cyclopenta[a]phenanthren-16-one C28 H44 O3 MDKJBHAILRWWEV-QIIHXXPTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.266 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.655	α = 96.73
b = 65.773	β = 99.62
c = 83.028	γ = 96.4

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-12 
Deposition Author(s): Koag, M.C., Monzingo, A.F., Cheun, Y., Lee, S.

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description