3ABH

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

• PDB DOI: https://doi.org/10.2210/pdb3ABH/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-12-11 Released: 2010-04-14 
• Deposition Author(s): Shimada, A., Shirouzu, M., Hanawa-Suetsugu, K., Terada, T., Umehara, T., Suetsugu, S., Yamamoto, M., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 20188097 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.94 kDa 
• Atom Count: 5,335 
• Modelled Residue Count: 576 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase C and casein kinase substrate in neurons protein 2	A, B	312	Homo sapiens	Mutation(s): 0  Gene Names: PACSIN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNF0 (Homo sapiens) Explore Q9UNF0  Go to UniProtKB:  Q9UNF0
PHAROS:  Q9UNF0 GTEx:  ENSG00000100266

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.522	α = 90
b = 86.145	β = 90
c = 353.051	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Shimada, A., Shirouzu, M., Hanawa-Suetsugu, K., Terada, T., Umehara, T., Suetsugu, S., Yamamoto, M., Yokoyama, S.

Revision History  

• 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
• Version 1.3: 2024-11-20
  Changes: Structure summary