4C69 | pdb_00004c69

ATP binding to murine voltage-dependent anion channel 1 (mVDAC1).

• PDB DOI: https://doi.org/10.2210/pdb4C69/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli M15
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2013-09-17 Released: 2014-06-04 
• Deposition Author(s): Paz, A., Colletier, J.P., Abramson, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Simulations Illuminate the Mechanism of ATP Transport Through Vdac1.

Choudhary, O.P., Paz, A., Adelman, J.L., Colletier, J., Abramson, J., Grabe, M.

(2014) Nat Struct Mol Biol 21: 626

• PubMed: 24908397 
• DOI: https://doi.org/10.1038/nsmb.2841
• Primary Citation Related Structures: 
  4C69


• PubMed Abstract: 
  

  The voltage-dependent anion channel (VDAC) mediates the flow of metabolites and ions across the outer mitochondrial membrane of all eukaryotic cells. The open channel passes millions of ATP molecules per second, whereas the closed state exhibits no detectable ATP flux. High-resolution structures of VDAC1 revealed a 19-stranded β-barrel with an α-helix partially occupying the central pore. To understand ATP permeation through VDAC, we solved the crystal structure of mouse VDAC1 (mVDAC1) in the presence of ATP, revealing a low-affinity binding site. Guided by these coordinates, we initiated hundreds of molecular dynamics simulations to construct a Markov state model of ATP permeation. These simulations indicate that ATP flows through VDAC through multiple pathways, in agreement with our structural data and experimentally determined physiological rates.

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Organizational Affiliation: 
• 1] Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania, USA. [2].
1] Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA. [2].
1] Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. [2].
1] Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France. [2] Centre National de la Recherche Scientifique, Institut de Biologie Structurale, Grenoble, France. [3] Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Direction des Sciences du Vivant, Institut de Biologie Structurale, Grenoble, France. [4].
1] Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA. [2] Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bangalore, India.
1] Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. [2] Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.44 kDa 
• Atom Count: 2,409 
• Modeled Residue Count: 283 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1	A [auth X]	295	Mus musculus	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q60932 (Mus musculus) Explore Q60932  Go to UniProtKB:  Q60932
IMPC:  MGI:106919

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MC3	C [auth X], F [auth X]	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE C36 H72 N O8 P CITHEXJVPOWHKC-UUWRZZSWSA-N
ATP	E [auth X]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
LDA	B [auth X], D [auth X], G [auth X], H [auth X], I [auth X], J [auth X]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.152	α = 90
b = 58.369	β = 99.25
c = 66.545	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Paz, A., Colletier, J.P., Abramson, J.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references
• Version 1.2: 2014-06-18
  Changes: Database references
• Version 1.3: 2014-07-16
  Changes: Database references
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description