2R1Q

Crystal Structure of Iodinated Human Saposin D in Space Group C2221


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of human saposins C and d: implications for lipid recognition and membrane interactions.

Rossmann, M.Schultz-Heienbrok, R.Behlke, J.Remmel, N.Alings, C.Sandhoff, K.Saenger, W.Maier, T.

(2008) Structure 16: 809-817

  • DOI: 10.1016/j.str.2008.02.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human saposins are essential proteins required for degradation of sphingolipids and lipid antigen presentation. Despite the conserved structural organization of saposins, their distinct modes of interaction with biological membranes are not fully und ...

    Human saposins are essential proteins required for degradation of sphingolipids and lipid antigen presentation. Despite the conserved structural organization of saposins, their distinct modes of interaction with biological membranes are not fully understood. We describe two crystal structures of human saposin C in an "open" configuration with unusual domain swapped homodimers. This form of SapC dimer supports the "clip-on" model for SapC-induced vesicle fusion. In addition, we present the crystal structure of SapD in two crystal forms. They reveal the monomer-monomer interface for the SapD dimer, which was confirmed in solution by analytical ultracentrifugation. The crystal structure of SapD suggests that side chains of Lys10 and Arg17 are involved in initial association with the preferred anionic biological membranes by forming salt bridges with sulfate or phosphate lipid headgroups.


    Organizational Affiliation

    Institut für Chemie und Biochemie, Kristallographie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proactivator polypeptide
A
85Homo 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
IYR
Query on IYR
A
L-PEPTIDE LINKINGC9 H10 I N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 40.465α = 90.00
b = 74.879β = 90.00
c = 66.791γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
AMoREphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description