4NQI

Structure of the N-terminal I-BAR domain (1-259) of D.Discoideum IBARa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The inverse BAR domain protein IBARa drives membrane remodeling to control osmoregulation, phagocytosis and cytokinesis.

Linkner, J.Witte, G.Zhao, H.Junemann, A.Nordholz, B.Runge-Wollmann, P.Lappalainen, P.Faix, J.

(2014) J.Cell.Sci. 127: 1279-1292

  • DOI: 10.1242/jcs.140756

  • PubMed Abstract: 
  • Here, we analyzed the single inverse Bin/Amphiphysin/Rvs (I-BAR) family member IBARa from Dictyostelium discoideum. The X-ray structure of the N-terminal I-BAR domain solved at 2.2 Å resolution revealed an all-α-helical structure that self-associates ...

    Here, we analyzed the single inverse Bin/Amphiphysin/Rvs (I-BAR) family member IBARa from Dictyostelium discoideum. The X-ray structure of the N-terminal I-BAR domain solved at 2.2 Å resolution revealed an all-α-helical structure that self-associates into a 165-Å zeppelin-shaped antiparallel dimer. The structural data are consistent with its shape in solution obtained by small-angle X-ray scattering. Cosedimentation, fluorescence anisotropy, and fluorescence and electron microscopy revealed that the I-BAR domain bound preferentially to phosphoinositide-containing vesicles and drove the formation of negatively curved tubules. Immunofluorescence labeling further showed accumulation of endogenous IBARa at the tips of filopodia, the rim of constricting phagocytic cups, in foci connecting dividing cells during the final stage of cytokinesis and most prominently at the osmoregulatory contractile vacuole (CV). Consistently, IBARa-null mutants displayed defects in CV formation and discharge, growth, phagocytosis and mitotic cell division, whereas filopodia formation was not compromised. Of note, IBARa-null mutants were also strongly impaired in cell spreading. Taken together, these data suggest that IBARa constitutes an important regulator of numerous cellular processes intimately linked with the dynamic rearrangement of cellular membranes.


    Organizational Affiliation

    Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SH3 domain-containing protein
A, B, C, D
264Dictyostelium discoideumMutation(s): 0 
Find proteins for C7FZZ0 (Dictyostelium discoideum)
Go to UniProtKB:  C7FZZ0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.100α = 90.00
b = 60.210β = 100.38
c = 147.620γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
SHARPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references