1N69

Crystal structure of human saposin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of saposin B reveals a dimeric shell for lipid binding

Ahn, V.E.Faull, K.F.Whitelegge, J.P.Fluharty, A.L.Prive, G.G.

(2003) Proc.Natl.Acad.Sci.USA 100: 38-43

  • DOI: 10.1073/pnas.0136947100

  • PubMed Abstract: 
  • Saposin B is a small, nonenzymatic glycosphingolipid activator protein required for the breakdown of cerebroside sulfates (sulfatides) within the lysosome. The protein can extract target lipids from membranes, forming soluble protein-lipid complexes ...

    Saposin B is a small, nonenzymatic glycosphingolipid activator protein required for the breakdown of cerebroside sulfates (sulfatides) within the lysosome. The protein can extract target lipids from membranes, forming soluble protein-lipid complexes that are recognized by arylsulfatase A. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity.


    Related Citations: 
    • Expression, purification, crystallization and preliminary X-ray analysis of recombinant human saposin B
      Ahn, V.E.,Faull, K.F.,Whitelegge, J.P.,Higginson, J.,Fluharty, A.L.,Prive, G.G.
      (2003) Protein Expr.Purif. 27: 186


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SAPOSIN B
A, B, C
81Homo 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
PEH
Query on PEH

Download SDF File 
Download CCD File 
A
DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.222 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.140α = 90.00
b = 72.140β = 90.00
c = 94.366γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
SHARPphasing
SCALAdata scaling
DMmodel building
SnBphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description