2D4C

Crystal structure of the endophilin BAR domain mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms

Masuda, M.Takeda, S.Sone, M.Ohki, T.Mori, H.Kamioka, Y.Mochizuki, N.

(2006) Embo J. 25: 2889-2897

  • DOI: 10.1038/sj.emboj.7601176
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crescent-shaped BAR (Bin/Amphiphysin/Rvs-homology) domain dimer is a versatile protein module that senses and generates positive membrane curvature. The BAR domain dimer of human endophilin-A1, solved at 3.1 A, has a unique structure consisting o ...

    The crescent-shaped BAR (Bin/Amphiphysin/Rvs-homology) domain dimer is a versatile protein module that senses and generates positive membrane curvature. The BAR domain dimer of human endophilin-A1, solved at 3.1 A, has a unique structure consisting of a pair of helix-loop appendages sprouting out from the crescent. The appendage's short helices form a hydrophobic ridge, which runs across the concave surface at its center. Examining liposome binding and tubulation in vitro using purified BAR domain and its mutants indicated that the ridge penetrates into the membrane bilayer and enhances liposome tubulation. BAR domain-expressing cells exhibited marked plasma membrane tubulation in vivo. Furthermore, a swinging-arm mutant lost liposome tubulation activity yet retaining liposome binding. These data suggested that the rigid crescent dimer shape is crucial for the tubulation. We here propose that the BAR domain drives membrane curvature by coordinate action of the crescent's scaffold mechanism and the ridge's membrane insertion in addition to membrane binding via amino-terminal amphipathic helix.


    Organizational Affiliation

    Department of Structural Analysis, National Cardiovascular Center Research Institute, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SH3-containing GRB2-like protein 2
A, B, C, D
256Homo sapiensMutation(s): 0 
Gene Names: SH3GL2 (CNSA2, SH3D2A)
Find proteins for Q99962 (Homo sapiens)
Go to Gene View: SH3GL2
Go to UniProtKB:  Q99962
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.344α = 90.00
b = 212.217β = 96.97
c = 54.317γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-10-13 
  • Released Date: 2006-07-11 
  • Deposition Author(s): Masuda, M., Takeda, S.

Revision History 

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance