4INQ

Crystal structure of Osh3 ORD in complex with PI(4)P from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

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This is version 1.1 of the entry. See complete history


Literature

Structure of osh3 reveals a conserved mode of phosphoinositide binding in oxysterol-binding proteins

Tong, J.Yang, H.Yang, H.Eom, S.H.Im, Y.J.

(2013) Structure 21: 1203-1213

  • DOI: https://doi.org/10.1016/j.str.2013.05.007
  • Primary Citation of Related Structures:  
    4IAP, 4IC4, 4INQ

  • PubMed Abstract: 

    The oxysterol-binding protein (OSBP)-related proteins (ORPs) are conserved from yeast to humans, and implicated in the regulation of lipid homeostasis and in signaling pathways. Saccharomyces cerevisiae has seven ORPs (Osh1-Osh7) that share one unknown essential function. Here, we report the 1.5-2.3 Å structures of the PH domain and ORD (OSBP-related domain) of yeast Osh3 in apo-form or in complex with phosphatidylinositol 4-phosphate (PI[4]P). Osh3 recognizes PI(4)P by the highly conserved residues in the tunnel of ORD whereas it lacks sterol binding due to the narrow hydrophobic tunnel. Yeast complementation tests suggest that PI(4)P binding to PH and ORD is essential for function. This study suggests that the unifying feature in all ORP homologs is the binding of PI(4)P to ORD and sterol binding is additional to certain homologs. Structural modeling of full-length Osh3 is consistent with the concept that Osh3 is a lipid transfer protein or regulator in membrane contact sites.


  • Organizational Affiliation

    College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterol-binding protein homolog 3397Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OSH3YHR073W
UniProt
Find proteins for P38713 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38713 
Go to UniProtKB:  P38713
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38713
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIF
Query on PIF

Download Ideal Coordinates CCD File 
B [auth A](2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate
C25 H48 O16 P2
SNIQYSSXZJPPEL-LKTRINTESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.889α = 90
b = 88.992β = 90
c = 95.665γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary