4DDJ

Crystal structure of saposin A in complex with lauryldimethylamine-N-oxide (LDAO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of saposin A lipoprotein discs.

Popovic, K.Holyoake, J.Pomes, R.Prive, G.G.

(2012) Proc.Natl.Acad.Sci.USA 109: 2908-2912

  • DOI: 10.1073/pnas.1115743109

  • PubMed Abstract: 
  • The saposins are small, membrane-active proteins that exist in both soluble and lipid-bound states. Saposin A has roles in sphingolipid catabolism and transport and is required for the breakdown of galactosylceramide by β-galactosylceramidase. In the ...

    The saposins are small, membrane-active proteins that exist in both soluble and lipid-bound states. Saposin A has roles in sphingolipid catabolism and transport and is required for the breakdown of galactosylceramide by β-galactosylceramidase. In the absence of lipid, saposin A adopts a closed monomeric apo conformation typical of this family. To study a lipid-bound state of this protein, we determined the crystal structure of saposin A in the presence of detergent to 1.9 Å resolution. The structure reveals two chains of saposin A in an open conformation encapsulating 40 internally bound detergent molecules organized in a highly ordered bilayer-like hydrophobic core. The complex provides a high-resolution view of a discoidal lipoprotein particle in which all of the internalized acyl chains are resolved. Saposin A lipoprotein discs exhibit limited selectivity with respect to the incorporated lipid, and can solubilize phospholipids, sphingolipids, and cholesterol into discrete, monodisperse particles with mass of approximately 27 kDa. These discs may be the smallest possible lipoprotein structures that are stabilized by lipid self-assembly.


    Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Saposin-A
A
83Homo sapiensMutation(s): 0 
Gene Names: PSAP (GLBA, SAP1)
Find proteins for P07602 (Homo sapiens)
Go to Gene View: PSAP
Go to UniProtKB:  P07602
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download SDF File 
Download CCD File 
A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 39.794α = 90.00
b = 39.794β = 90.00
c = 247.284γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references
  • Version 1.2: 2012-03-14
    Type: Database references