1O6U | pdb_00001o6u

The Crystal Structure of Human Supernatant Protein Factor

• PDB DOI: https://doi.org/10.2210/pdb1O6U/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-10-16 Released: 2003-10-17 
• Deposition Author(s): Stocker, A., Schulze-Briese, C., Tomizaki, T.

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Experimental Data Snapshot

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

Literature

Crystal Structure of Human Supernatant Protein Factor

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

(2002) Structure 10: 1533

• PubMed: 12429094 
• DOI: https://doi.org/10.1016/s0969-2126(02)00884-5
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, Bern, Switzerland. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 140.94 kDa 
• Atom Count: 10,203 
• Modeled Residue Count: 1,178 
• Deposited Residue Count: 1,209 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEC14-LIKE PROTEIN 2	A, B [auth C], C [auth E]	403	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O76054 (Homo sapiens) Explore O76054  Go to UniProtKB:  O76054
PHAROS:  O76054 GTEx:  ENSG00000100003

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	D [auth A], E [auth C], F [auth E]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B [auth C], C [auth E]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

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

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.794	α = 116.26
b = 84.24	β = 102.39
c = 87.111	γ = 99.87

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-17 
Deposition Author(s): Stocker, A., Schulze-Briese, C., Tomizaki, T.

Revision History  

• 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