4J7Q

Crystal structure of Saccharomyces cerevisiae Sfh3 complexed with phosphatidylinositol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural determinants for phosphatidylinositol recognition by Sfh3 and substrate-induced dimer-monomer transition during lipid transfer cycles.

Yang, H.Tong, J.Leonard, T.A.Im, Y.J.

(2013) FEBS Lett 587: 1610-1616

  • DOI: 10.1016/j.febslet.2013.04.009
  • Primary Citation of Related Structures:  
    4J7P, 4J7Q

  • PubMed Abstract: 
  • Sec14 family homologs are the major yeast phosphatidylinositol/phosphatidylcholine transfer proteins regulating lipid metabolism and vesicle trafficking. The structure of Saccharomyces cerevisiae Sfh3 displays a conserved Sec14 scaffold and reveals determinants for the specific recognition of phosphatidylinositol ligand ...

    Sec14 family homologs are the major yeast phosphatidylinositol/phosphatidylcholine transfer proteins regulating lipid metabolism and vesicle trafficking. The structure of Saccharomyces cerevisiae Sfh3 displays a conserved Sec14 scaffold and reveals determinants for the specific recognition of phosphatidylinositol ligand. Apo-Sfh3 forms a dimer through the hydrophobic interaction of gating helices. Binding of phosphatidylinositol leads to dissociation of the dimer into monomers in a reversible manner. This study suggests that the substrate induced dimer-monomer transformation is an essential part of lipid transfer cycles by Sfh3.


    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
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol transfer protein PDR16A, B333Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: N1158PDR16SFH3YNL231C
UniProt
Find proteins for P53860 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53860 
Go to UniProtKB:  P53860
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53860
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B7N
Query on B7N

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C45 H85 O13 P
YOBFISPJJWPPTK-BAAZTTAESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.889α = 90
b = 144.149β = 111.28
c = 55.656γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata 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: 2013-07-03
    Type: Initial release