Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 32.18 kDa 
• Atom Count: 2207 
• Modelled Residue Count: 288 
• Deposited Residue Count: 294 
• Unique protein chains: 1

2JK4

Structure of the human voltage-dependent anion channel

• PDB DOI: 10.2210/pdb2JK4/pdb

• Classification: TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2008-08-15 Released: 2008-10-14 
• Deposition Author(s): Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Griesinger, C., Zweckstetter, M., Zeth, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.387 
• R-Value Work: 0.325 
• R-Value Observed: 0.331 

Literature

Structure of the Human Voltage-Dependent Anion Channel.

Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Griesinger, C., Zweckstetter, M., Zeth, K.

(2008) Proc Natl Acad Sci U S A 105: 15370

• PubMed: 18832158 
• DOI: 10.1073/pnas.0808115105
• Primary Citation of Related Structures:  
  2JK4


• PubMed Abstract: 
  

The voltage-dependent anion channel (VDAC), also known as mitochondrial porin, is the most abundant protein in the mitochondrial outer membrane (MOM). VDAC is the channel known to guide the metabolic flux across the MOM and plays a key role in mitochondrially induced apoptosis. Here, we present the 3D structure of human VDAC1, which was solved conjointly by NMR spectroscopy and x-ray crystallography. Human VDAC1 (hVDAC1) adopts a beta-barrel architecture composed of 19 beta-strands with an alpha-helix located horizontally midway within the pore. Bioinformatic analysis indicates that this channel architecture is common to all VDAC proteins and is adopted by the general import pore TOM40 of mammals, which is also located in the MOM.

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Organizational Affiliation: 

Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1	A	294	Homo sapiens	Mutation(s): 0  Gene Names: VDAC1, VDAC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P21796 (Homo sapiens) Explore P21796  Go to UniProtKB:  P21796
PHAROS:  P21796 GTEx:  ENSG00000213585

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.387 
• R-Value Work: 0.325 
• R-Value Observed: 0.331 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.99	α = 90
b = 77.99	β = 90
c = 167.04	γ = 120

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XDS	data reduction
SCALA	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-15 
• Released Date: 2008-10-14 
Deposition Author(s): Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Griesinger, C., Zweckstetter, M., Zeth, K.

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance