4J7Q | pdb_00004j7q

Crystal structure of Saccharomyces cerevisiae Sfh3 complexed with phosphatidylinositol

• PDB DOI: https://doi.org/10.2210/pdb4J7Q/pdb

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


• Deposited: 2013-02-14 Released: 2013-07-03 
• Deposition Author(s): Yang, H., Im, Y.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

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

• PubMed: 23603387 
• DOI: https://doi.org/10.1016/j.febslet.2013.04.009
• Primary Citation 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. 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.

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Organizational Affiliation: 
• College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.94 kDa 
• Atom Count: 5,736 
• Modeled Residue Count: 644 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol transfer protein PDR16	A, B	333	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: N1158, PDR16, SFH3, YNL231C
UniProt
Find proteins for P53860 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53860  Go to UniProtKB:  P53860

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B7N	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.889	α = 90
b = 144.149	β = 111.28
c = 55.656	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Yang, H., Im, Y.J.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations