3BQQ

Crystal Structure of Human Saposin D (triclinic)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structures of the human ceramide activator protein saposin D.

Popovic, K.Prive, G.G.

(2008) Acta Crystallogr D Biol Crystallogr 64: 589-594

  • DOI: https://doi.org/10.1107/S0907444908003120
  • Primary Citation of Related Structures:  
    3BQP, 3BQQ

  • PubMed Abstract: 

    Saposin D is a sphingolipid activator protein required for the lysosomal breakdown of ceramide to a fatty acid and sphingosine by acid ceramidase. The crystal structure of saposin D has been determined in two different crystal forms, resulting in a total of six crystallographically independent views of this small 80-amino-acid protein. All of the structures are highly similar and reveal the monomeric form of the saposin fold previously seen in the crystal structures of saposins A and C. Saposin D is slightly more compact than the related saposins A and C owing to a slight repositioning of the 'stem' and 'hairpin' regions of the protein.


  • Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROACTIVATOR POLYPEPTIDEA [auth C],
B [auth A],
C [auth B],
D
80Homo sapiensMutation(s): 0 
Gene Names: PSAP
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.66α = 89.9
b = 41.12β = 81.2
c = 65.45γ = 71.4
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary