5XDN

Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1

Hosaka, T.Okazaki, M.Kimura-Someya, T.Ishizuka-Katsura, Y.Ito, K.Yokoyama, S.Dodo, K.Sodeoka, M.Shirouzu, M.

(2017) Protein Sci. 26: 1749-1758

  • DOI: 10.1002/pro.3211
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, l ...

    Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad-range screening using a bicelle crystallization method produced crystals in space groups C222 and P221 21 , which diffracted to a resolution of 3.10 and 3.15 Å, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P221 21 were oriented anti-parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with β-strands, hydrophilic interactions with loop regions, and protein-lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo- or hetero-oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis-regulating proteins in the Bcl-2 family.


    Organizational Affiliation

    Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Voltage-dependent anion-selective channel protein 1
A, B
295Homo sapiensMutation(s): 0 
Gene Names: VDAC1 (VDAC)
Find proteins for P21796 (Homo sapiens)
Go to Gene View: VDAC1
Go to UniProtKB:  P21796
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCT
Query on OCT

Download SDF File 
Download CCD File 
A
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
D12
Query on D12

Download SDF File 
Download CCD File 
A, B
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

Download SDF File 
Download CCD File 
B
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

Download SDF File 
Download CCD File 
A, B
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.266 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.700α = 90.00
b = 84.960β = 90.00
c = 146.230γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Database references