3I2W

Crystal structure of EFC/F-BAR domain of Drosophila Syndapin/PACSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural requirements for PACSIN/Syndapin operation during zebrafish embryonic notochord development.

Edeling, M.A.Sanker, S.Shima, T.Umasankar, P.K.Honing, S.Kim, H.Y.Davidson, L.A.Watkins, S.C.Tsang, M.Owen, D.J.Traub, L.M.

(2009) PLoS One 4: e8150-e8150

  • DOI: https://doi.org/10.1371/journal.pone.0008150
  • Primary Citation of Related Structures:  
    3I2W

  • PubMed Abstract: 

    PACSIN/Syndapin proteins are membrane-active scaffolds that participate in endocytosis. The structure of the Drosophila Syndapin N-terminal EFC domain reveals a crescent shaped antiparallel dimer with a high affinity for phosphoinositides and a unique membrane-inserting prong upon the concave surface. Combined structural, biochemical and reverse genetic approaches in zebrafish define an important role for Syndapin orthologue, Pacsin3, in the early formation of the notochord during embryonic development. In pacsin3-morphant embryos, midline convergence of notochord precursors is defective as axial mesodermal cells fail to polarize, migrate and differentiate properly. The pacsin3 morphant phenotype of a stunted body axis and contorted trunk is rescued by ectopic expression of Drosophila Syndapin, and depends critically on both the prong that protrudes from the surface of the bowed Syndapin EFC domain and the ability of the antiparallel dimer to bind tightly to phosphoinositides. Our data confirm linkage between directional migration, endocytosis and cell specification during embryonic morphogenesis and highlight a key role for Pacsin3 in this coupling in the notochord.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Syndapin
A, B
290Drosophila melanogasterMutation(s): 0 
Gene Names: CG33094Dmel_CG33094Syndsyndapin
UniProt
Find proteins for Q9VDI1 (Drosophila melanogaster)
Explore Q9VDI1 
Go to UniProtKB:  Q9VDI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VDI1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.595α = 90
b = 85.525β = 90
c = 192.86γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance