Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.65 kDa 
• Atom Count: 991 
• Modelled Residue Count: 80 
• Deposited Residue Count: 83 
• Unique protein chains: 1

 4DDJ

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

• PDB DOI: 10.2210/pdb4DDJ/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2012-01-18 Released: 2012-02-15 
• Deposition Author(s): Popovic, K., Prive, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.280 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Structure of saposin A lipoprotein discs.

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

(2012) Proc Natl Acad Sci U S A 109: 2908-2912

• PubMed: 22308394 
• DOI: 10.1073/pnas.1115743109
• Primary Citation of Related Structures:  
  4DDJ


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saposin-A	A	83	Homo sapiens	Mutation(s): 0  Gene Names: PSAP, GLBA, SAP1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P07602 (Homo sapiens) Explore P07602  Go to UniProtKB:  P07602
PHAROS:  P07602

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LDA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.280 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.794	α = 90
b = 39.794	β = 90
c = 247.284	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Popovic, K., Prive, G.G.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-02-22
  Changes: Database references
• Version 1.2: 2012-03-14
  Changes: Database references
• Version 1.3: 2020-01-29
  Changes: Advisory, Database references, Derived calculations