6G73

The dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 3.3 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6G73/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-04-04 Released: 2019-04-24 
• Deposition Author(s): Razeto, A., Gribbon, P., Loew, C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 0.298 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

The dynamic nature of the VDAC1 channels in bilayers as revealed by two crystal structures of the human isoform in bicelles at 2.7 and 3.3 Angstrom resolution: implications for VDAC1 voltage-dependent mechanism and for its oligomerization

Razeto, A., Gribbon, P., Loew, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 130.9 kDa 
• Atom Count: 8,753 
• Modelled Residue Count: 1,126 
• Deposited Residue Count: 1,164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent anion-selective channel protein 1	A, B, C, D	291	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MC3	E [auth A], F [auth A], G [auth B], H [auth B], I [auth D]	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE C36 H72 N O8 P CITHEXJVPOWHKC-UUWRZZSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 0.298 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.22	α = 90
b = 83.36	β = 90.59
c = 156.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Razeto, A., Gribbon, P., Loew, C.

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Funding Organization	Location	Grant Number
Other private	Germany	--

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Derived calculations
• Version 1.2: 2019-07-10
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description