1O6U

The Crystal Structure of Human Supernatant Protein Factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Human Supernatant Protein Factor

Stocker, A.Tomizaki, T.Schulze-Briese, C.Baumann, U.

(2002) Structure 10: 1533

  • DOI: https://doi.org/10.1016/s0969-2126(02)00884-5
  • Primary Citation of Related Structures:  
    1O6U

  • PubMed Abstract: 

    Supernatant protein factor (SPF) promotes the epoxidation of squalene catalyzed by microsomes. Several studies suggest its in vivo role in the cholesterol biosynthetic pathway by a yet unknown mechanism. SPF belongs to a family of lipid binding proteins called CRAL_TRIO, which include yeast phosphatidylinositol transfer protein Sec14 and tocopherol transfer protein TTP. The crystal structure of human SPF at a resolution of 1.9 A reveals a two domain topology. The N-terminal 275 residues form a Sec14-like domain, while the C-terminal 115 residues consist of an eight-stranded jelly-roll barrel similar to that found in many viral protein structures. The ligand binding cavity has a peculiar horseshoe-like shape. Contrary to the Sec14 crystal structure, the lipid-exchange loop is in a closed conformation, suggesting a mechanism for lipid exchange.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, Bern, Switzerland. achim.stocker@ibc.unibe.ch


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SEC14-LIKE PROTEIN 2A,
B [auth C],
C [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
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
B [auth C],
C [auth E]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.794α = 116.26
b = 84.24β = 102.39
c = 87.111γ = 99.87
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-17
    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: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary