4IAP

Crystal structure of PH domain of Osh3 from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.str.2013.05.007
  • Primary Citation of Related Structures:  

  • 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 unkno ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterol-binding protein homolog 3,Endolysin,Oxysterol-binding protein homolog 3
A, B
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Enterobacteria phage T4
This entity is chimeric
Mutation(s): 3 
Gene Names: OSH3, E
EC: 3.2.1.17
Find proteins for P38713 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38713
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.033α = 90.00
b = 91.307β = 81.42
c = 84.130γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
HKL-2000data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-12-07 
  • Released Date: 2013-07-31 
  • Deposition Author(s): Tong, J., Im, Y.J.

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Source and taxonomy
  • Version 1.2: 2017-06-21
    Type: Database references, Source and taxonomy, Structure summary