1N69 | pdb_00001n69

Crystal structure of human saposin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.262 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 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 U S A 100: 38-43

  • DOI: https://doi.org/10.1073/pnas.0136947100
  • Primary Citation Related Structures: 
    1N69

  • 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 28.13 kDa 
  • Atom Count: 1,955 
  • Modeled Residue Count: 236 
  • Deposited Residue Count: 243 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SAPOSIN B
A, B, C
81Homo sapiensMutation(s): 0 
Gene Names: ProsaposinPSAP
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07602
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
D [auth A]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.262 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.14α = 90
b = 72.14β = 90
c = 94.366γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
DMmodel building
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2021-06-30
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary