The Crystal Structure of Mouse VDAC1 at 2.3 A resolution

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

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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 U S A 105: 17742-17747

  • DOI: https://doi.org/10.1073/pnas.0809634105
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent anion-selective channel protein 1A [auth X]295Mus musculusMutation(s): 0 
Gene Names: Vdac1Vdac5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q60932 (Mus musculus)
Explore Q60932 
Go to UniProtKB:  Q60932
IMPC:  MGI:106919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60932
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MC3

Download Ideal Coordinates CCD File 
C36 H72 N O8 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.23α = 90
b = 58.39β = 99.25
c = 66.58γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations