3EMN

The Crystal Structure of Mouse VDAC1 at 2.3 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of mouse VDAC1 at 2.3 A resolution reveals mechanistic insights into metabolite gating

Ujwal, R.Cascio, D.Colletier, J.P.Faham, S.Zhang, J.Toro, L.Ping, P.Abramson, J.

(2008) Proc.Natl.Acad.Sci.USA 105: 17742-17747

  • DOI: 10.1073/pnas.0809634105

  • PubMed Abstract: 
  • The voltage-dependent anion channel (VDAC) constitutes the major pathway for the entry and exit of metabolites across the outer membrane of the mitochondria and can serve as a scaffold for molecules that modulate the organelle. We report the crystal ...

    The voltage-dependent anion channel (VDAC) constitutes the major pathway for the entry and exit of metabolites across the outer membrane of the mitochondria and can serve as a scaffold for molecules that modulate the organelle. We report the crystal structure of a beta-barrel eukaryotic membrane protein, the murine VDAC1 (mVDAC1) at 2.3 A resolution, revealing a high-resolution image of its architecture formed by 19 beta-strands. Unlike the recent NMR structure of human VDAC1, the position of the voltage-sensing N-terminal segment is clearly resolved. The alpha-helix of the N-terminal segment is oriented against the interior wall, causing a partial narrowing at the center of the pore. This segment is ideally positioned to regulate the conductance of ions and metabolites passing through the VDAC pore.


    Organizational Affiliation

    Department of Physiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Voltage-dependent anion-selective channel protein 1
X
295Mus musculusMutation(s): 0 
Gene Names: Vdac1 (Vdac5)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
Protein: 
VDAC-1 voltage dependent anion channel
Find proteins for Q60932 (Mus musculus)
Go to UniProtKB:  Q60932
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MC3
Query on MC3

Download SDF File 
Download CCD File 
X
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.230α = 90.00
b = 58.390β = 99.25
c = 66.580γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
DMphasing
XSCALEdata scaling
MLPHAREphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance