3B7Z

Crystal Structure of Yeast Sec14 Homolog Sfh1 in Complex with Phosphatidylcholine or Phosphatidylinositol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Functional anatomy of phospholipid binding and regulation of phosphoinositide homeostasis by proteins of the sec14 superfamily

Schaaf, G.Ortlund, E.A.Tyeryar, K.R.Mousley, C.J.Ile, K.E.Garrett, T.A.Ren, J.Woolls, M.J.Raetz, C.R.Redinbo, M.R.Bankaitis, V.A.

(2008) Mol Cell 29: 191-206

  • DOI: https://doi.org/10.1016/j.molcel.2007.11.026
  • Primary Citation of Related Structures:  
    3B74, 3B7N, 3B7Q, 3B7Z

  • PubMed Abstract: 

    Sec14, the major yeast phosphatidylinositol (PtdIns)/phosphatidylcholine (PtdCho) transfer protein, regulates essential interfaces between lipid metabolism and membrane trafficking from the trans-Golgi network (TGN). How Sec14 does so remains unclear. We report that Sec14 binds PtdIns and PtdCho at distinct (but overlapping) sites, and both PtdIns- and PtdCho-binding activities are essential Sec14 activities. We further show both activities must reside within the same molecule to reconstitute a functional Sec14 and for effective Sec14-mediated regulation of phosphoinositide homeostasis in vivo. This regulation is uncoupled from PtdIns-transfer activity and argues for an interfacial presentation mode for Sec14-mediated potentiation of PtdIns kinases. Such a regulatory role for Sec14 is a primary counter to action of the Kes1 sterol-binding protein that antagonizes PtdIns 4-OH kinase activity in vivo. Collectively, these findings outline functional mechanisms for the Sec14 superfamily and reveal additional layers of complexity for regulating phosphoinositide homeostasis in eukaryotes.


  • Organizational Affiliation

    Department of Cell and Developmental Biology, School of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7090, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YKL091C320Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33324 
Go to UniProtKB:  P33324
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33324
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B7N
Query on B7N

Download Ideal Coordinates CCD File 
B [auth A](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
6PL
Query on 6PL

Download Ideal Coordinates CCD File 
C [auth A](4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-RRHRGVEJSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.354α = 90
b = 72.931β = 90
c = 97.594γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
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: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2018-02-14
    Changes: Experimental preparation
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations