4OMK

Crystal structure of SPF bound to squalene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights on cholesterol endosynthesis: Binding of squalene and 2,3-oxidosqualene to supernatant protein factor.

Christen, M.Marcaida, M.J.Lamprakis, C.Aeschimann, W.Vaithilingam, J.Schneider, P.Hilbert, M.Schneider, G.Cascella, M.Stocker, A.

(2015) J.Struct.Biol. 190: 261-270

  • DOI: 10.1016/j.jsb.2015.05.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We present the crystal structures of the SEC14-like domain of supernatant protein factor (SPF) in complex with squalene and 2,3-oxidosqualene. The structures were resolved at 1.75Å (complex with squalene) and 1.6Å resolution (complex with 2,3-oxidosq ...

    We present the crystal structures of the SEC14-like domain of supernatant protein factor (SPF) in complex with squalene and 2,3-oxidosqualene. The structures were resolved at 1.75Å (complex with squalene) and 1.6Å resolution (complex with 2,3-oxidosqualene), leading in both cases to clear images of the protein/substrate interactions. Ligand binding is facilitated by removal of the Golgi-dynamics (GOLD) C-terminal domain of SPF, which, as shown in previous structures of the apo-protein, blocked the opening of the binding pocket to the exterior. Both substrates bind into a large hydrophobic cavity, typical of such lipid-transporter family. Our structures report no specific recognition mode for the epoxide group. In fact, for both molecules, ligand affinity is dominated by hydrophobic interactions, and independent investigations by computational models or differential scanning micro-calorimetry reveal similar binding affinities for both ligands. Our findings elucidate the molecular bases of the role of SPF in sterol endo-synthesis, supporting the original hypothesis that SPF is a facilitator of substrate flow within the sterol synthetic pathway. Moreover, our results suggest that the GOLD domain acts as a regulator, as its conformational displacement must occur to favor ligand binding and release during the different synthetic steps.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SEC14-like protein 2
A, B
278Homo sapiensMutation(s): 0 
Gene Names: SEC14L2 (C22orf6, KIAA1186, KIAA1658)
Find proteins for O76054 (Homo sapiens)
Go to Gene View: SEC14L2
Go to UniProtKB:  O76054
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
SQL
Query on SQL

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Download CCD File 
A, B
(6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene
squalene
C30 H50
YYGNTYWPHWGJRM-AAJYLUCBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.270α = 90.00
b = 73.540β = 96.88
c = 94.230γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references