1OLM | pdb_00001olm

Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.211 (Depositor) 
  • R-Value Work: 
    0.180 (Depositor) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1OLM

This is version 1.3 of the entry. See complete history

Literature

Supernatant Protein Factor in Complex with Rrr-Alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis

Stocker, A.Baumann, U.

(2003) J Mol Biology 332: 759

  • DOI: https://doi.org/10.1016/s0022-2836(03)00924-0
  • Primary Citation Related Structures: 
    1OLM

  • PubMed Abstract: 

    The vast majority of monomeric lipid transport in nature is performed by lipid-specific protein carriers. This class of proteins can enclose cognate lipid molecules in a hydrophobic cavity and transport them across the aqueous environment. Supernatant protein factor (SPF) is an enigmatic representative of monomeric lipid transporters belonging to the SEC14 family. SPF stimulates squalene epoxidation, a downstream step of the cholesterol biosynthetic pathway, by an unknown mechanism. Here, we present the three-dimensional crystal structure of human SPF in complex with RRR-alpha-tocopherylquinone, the major physiological oxidation product of RRR-alpha-tocopherol, at a resolution of 1.95A. The structure of the complex reveals how SPF sequesters RRR-alpha-tocopherylquinone (RRR-alpha-TQ) in its protein body and permits a comparison with the recently solved structure of human alpha-tocopherol transfer protein (alpha-TTP) in complex with RRR-alpha-tocopherol. Recent findings have shown that RRR-alpha-TQ is reduced in vivo to RRR-alpha-TQH(2), the latter has been suggested to protect low-density lipoprotein (LDL) particles from oxidation. Hence, the antioxidant function of the redox couple RRR-alpha-TQ/RRR-alpha-TQH(2) in blocking LDL oxidation may reduce cellular cholesterol uptake and thus explain how SPF upregulates cholesterol synthesis.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Berne, 3012 Bern, Switzerland. achim.stocker@ibc.unibe.ch

Macromolecule Content 

  • Total Structure Weight: 139.99 kDa 
  • Atom Count: 10,464 
  • Modeled Residue Count: 1,177 
  • Deposited Residue Count: 1,209 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SEC14-LIKE PROTEIN 2A,
B [auth C]
403Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O76054 (Homo sapiens)
Explore O76054 
Go to UniProtKB:  O76054
PHAROS:  O76054
GTEx:  ENSG00000100003 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76054
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SEC14-LIKE PROTEIN 2C [auth E]403Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O76054 (Homo sapiens)
Explore O76054 
Go to UniProtKB:  O76054
PHAROS:  O76054
GTEx:  ENSG00000100003 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76054
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.211 (Depositor) 
  • R-Value Work:  0.180 (Depositor) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.856α = 116.2
b = 84.621β = 102.64
c = 87.452γ = 100.24
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references