2DOB

Crystal Structure of Human Saposin A

• PDB DOI: https://doi.org/10.2210/pdb2DOB/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2006-04-28 Released: 2006-07-25 
• Deposition Author(s): Prive, G.G., Ahn, V.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Crystal structures of saposins A and C.

Ahn, V.E., Leyko, P., Alattia, J.R., Chen, L., Prive, G.G.

(2006) Protein Sci 15: 1849-1857

• PubMed: 16823039 
• DOI: https://doi.org/10.1110/ps.062256606
• Primary Citation of Related Structures:  
  2DOB, 2GTG


• PubMed Abstract: 
  

  Saposins A and C are sphingolipid activator proteins required for the lysosomal breakdown of galactosylceramide and glucosylceramide, respectively. The saposins interact with lipids, leading to an enhanced accessibility of the lipid headgroups to their cognate hydrolases. We have determined the crystal structures of human saposins A and C to 2.0 Angstroms and 2.4 Angstroms, respectively, and both reveal the compact, monomeric saposin fold. We confirmed that these two proteins were monomeric in solution at pH 7.0 by analytical centrifugation. However, at pH 4.8, in the presence of the detergent C(8)E(5), saposin A assembled into dimers, while saposin C formed trimers. Saposin B was dimeric under all conditions tested. The self-association of the saposins is likely to be relevant to how these small proteins interact with lipids, membranes, and hydrolase enzymes.

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Organizational Affiliation: 

Department of Medical Biophysics, University of Toronto, Canada.

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.24 kDa 
• Atom Count: 686 
• Modelled Residue Count: 82 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proactivator polypeptide	A	83	Homo sapiens	Mutation(s): 3  Gene Names: PSAP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P07602 (Homo sapiens) Explore P07602  Go to UniProtKB:  P07602
PHAROS:  P07602 GTEx:  ENSG00000197746

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.68	α = 90
b = 50.04	β = 90
c = 33.82	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-25 
Deposition Author(s): Prive, G.G., Ahn, V.E.

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary