4BUM

Crystal structure of the Voltage Dependant Anion Channel 2 from zebrafish.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-Resolution Structure and Double Electron-Electron Resonance of the Zebrafish Voltage Dependent Anion Channel 2 Reveal an Oligomeric Population.

Schredelseker, J.Paz, A.Lopez, C.J.Altenbach, C.Leung, C.S.Drexler, M.K.Chen, J.Hubbell, W.L.Abramson, J.

(2014) J.Biol.Chem. 289: 12566

  • DOI: 10.1074/jbc.M113.497438

  • PubMed Abstract: 
  • In recent years, there has been a vast increase in structural and functional understanding of VDAC1, but VDAC2 and -3 have been understudied despite having many unique phenotypes. One reason for the paucity of structural and biochemical characterizat ...

    In recent years, there has been a vast increase in structural and functional understanding of VDAC1, but VDAC2 and -3 have been understudied despite having many unique phenotypes. One reason for the paucity of structural and biochemical characterization of the VDAC2 and -3 isoforms stems from the inability of obtaining purified, functional protein. Here we demonstrate the expression, isolation, and basic characterization of zebrafish VDAC2 (zfVDAC2). Further, we resolved the structure of zfVDAC2 at 2.8 Å resolution, revealing a crystallographic dimer. The dimer orientation was confirmed in solution by double electron-electron resonance spectroscopy and by cross-linking experiments disclosing a dimer population of ∼20% in lauryldimethine amine oxide detergent micelles, whereas in lipidic bicelles a higher population of dimeric and higher order oligomers species were observed. The present study allows for a more accurate structural comparison between VDAC2 and its better-studied counterpart VDAC1.


    Organizational Affiliation

    From the Department of Molecular, Cell and Developmental Biology.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VOLTAGE-DEPENDENT ANION CHANNEL 2
X
289Danio rerioMutation(s): 0 
Gene Names: vdac2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
Protein: 
VDAC-2 voltage dependent anion channel
Find proteins for Q8AWD0 (Danio rerio)
Go to UniProtKB:  Q8AWD0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download SDF File 
Download CCD File 
X
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.470α = 90.00
b = 72.470β = 90.00
c = 177.950γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Structure summary
  • Version 1.2: 2014-05-14
    Type: Database references