Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.0 A)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

Starting Model: experimental
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Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II

Shimada, A.Takano, K.Shirouzu, M.Hanawa-Suetsugu, K.Terada, T.Toyooka, K.Umehara, T.Yamamoto, M.Yokoyama, S.Suetsugu, S.

(2010) FEBS Lett 584: 1111-1118

  • DOI: https://doi.org/10.1016/j.febslet.2010.02.058
  • Primary Citation of Related Structures:  
    3ABH, 3ACO

  • PubMed Abstract: 

    The extended Fes-CIP4 homology (EFC)/FCH-BAR (F-BAR) domain tubulates membranes. Overexpression of the pacsin2 EFC/F-BAR domain resulted in tubular localization inside cells and deformed liposomes into tubules in vitro. We found that overexpression of the pacsin2 EFC/F-BAR domain induced cellular microspikes, with the pacsin2 EFC/F-BAR domain concentrated at the neck. The hydrophobic loops and the basic amino-acid residues on the concave surface of the pacsin2 EFC/F-BAR domain are essential for both the microspike formation and tubulation. Since the curvature of the neck of the microspike and that of the tubulation share similar geometry, the pacsin2 EFC/F-BAR domain is considered to facilitate both microspike formation and tubulation.

  • Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase C and casein kinase substrate in neurons protein 2
A, B
312Homo sapiensMutation(s): 0 
Gene Names: PACSIN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNF0 (Homo sapiens)
Explore Q9UNF0 
Go to UniProtKB:  Q9UNF0
GTEx:  ENSG00000100266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNF0
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.522α = 90
b = 86.145β = 90
c = 353.051γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-14
    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