4F4B | pdb_00004f4b

Structure of OSH4 with a cholesterol analog

• PDB DOI: https://doi.org/10.2210/pdb4F4B/pdb

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


• Deposited: 2012-05-10 Released: 2013-05-15 
• Deposition Author(s): Koag, M.C., Monzingo, A.F., Cheun, Y., Lee, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.271 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

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 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.

---

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: 100.62 kDa 
• Atom Count: 7,052 
• Modeled Residue Count: 847 
• 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
L39	C [auth A], D [auth B]	(3beta,9beta,25R)-3-hydroxy-26-iodocholest-5-ene-16,22-dione C27 H41 I O3 AWHQELOUIOILMT-WQTURIIHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.271 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.123	α = 96.56
b = 65.397	β = 100.28
c = 82.314	γ = 95.91

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: 2013-05-15 
Deposition Author(s): Koag, M.C., Monzingo, A.F., Cheun, Y., Lee, S.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations