6W32

Crystal structure of Sfh5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins.

Khan, D.Lee, D.Gulten, G.Aggarwal, A.Wofford, J.Krieger, I.Tripathi, A.Patrick, J.W.Eckert, D.M.Laganowsky, A.Sacchettini, J.Lindahl, P.Bankaitis, V.A.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.57081
  • Primary Citation of Related Structures:  
    6W32

  • PubMed Abstract: 

    Yeast Sfh5 is an unusual member of the Sec14-like phosphatidylinositol transfer protein (PITP) family. Whereas PITPs are defined by their abilities to transfer phosphatidylinositol between membranes in vitro, and to stimulate phosphoinositide signaling in vivo, Sfh5 does not exhibit these activities. Rather, Sfh5 is a redox-active penta-coordinate high spin Fe III hemoprotein with an unusual heme-binding arrangement that involves a co-axial tyrosine/histidine coordination strategy and a complex electronic structure connecting the open shell iron d -orbitals with three aromatic ring systems. That Sfh5 is not a PITP is supported by demonstrations that heme is not a readily exchangeable ligand, and that phosphatidylinositol-exchange activity is resuscitated in heme binding-deficient Sfh5 mutants. The collective data identify Sfh5 as the prototype of a new class of fungal hemoproteins, and emphasize the versatility of the Sec14-fold as scaffold for translating the binding of chemically distinct ligands to the control of diverse sets of cellular activities.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol transfer protein SFH5A [auth B],
B [auth A],
C
304Saccharomyces cerevisiae YJM789Mutation(s): 0 
Gene Names: SFH5SCY_3146
Membrane Entity: Yes 
UniProt
Find proteins for P47008 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47008 
Go to UniProtKB:  P47008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47008
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.343α = 90
b = 205.343β = 90
c = 68.313γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
XDSdata reduction
Aimlessdata scaling
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references