9GNG | pdb_00009gng

mouse VDAC1 in complex with MPD

• PDB DOI: https://doi.org/10.2210/pdb9GNG/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-09-03 Released: 2025-01-08 
• Deposition Author(s): Lolicato, M., Arrigoni, C.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.298 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Protocol for high-yield bacterial expression and purification of the voltage-dependent anion channel 1 for high-throughput biophysical assays.

Conti Nibali, S., Magri, A., Messina, A., Wagner, A., Duman, R., De Pinto, V., Turato, C., Arrigoni, C., Lolicato, M.

(2025) STAR Protoc 6: 103557-103557

• PubMed: 39799574 
• DOI: https://doi.org/10.1016/j.xpro.2024.103557
• Primary Citation of Related Structures:  
  9GNG


• PubMed Abstract: 
  

  Voltage-dependent anion channel 1 (VDAC1) is a key protein in cellular metabolism and apoptosis. Here, we present a protocol to express and purify milligram amounts of recombinant VDAC1 in Escherichia coli. We detail steps for a fluorescence polarization-based high-throughput screening assay using NADH displacement, along with procedures for thermostability, fluorescence polarization, and X-ray crystallography. In this context, we demonstrate how 2-methyl-2,4-pentanediol (MPD), a crystallization reagent, interferes with VDAC1 small-molecule binding, hindering the detection of these ligands in the crystal. For complete details on the use and execution of this protocol, please refer to Conti Nibali et al. ¹ .

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Organizational Affiliation: 
• Department of Molecular Medicine, University of Pavia, Pavia, Italy.
Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy.
Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE Didcot, UK.
Department of Biomedical and Biotechnological Sciences, Section of Biology & Genetics, University of Catania, Catania, Italy.
Department of Molecular Medicine, University of Pavia, Pavia, Italy. Electronic address: [e-mail].
Department of Molecular Medicine, University of Pavia, Pavia, Italy. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.99 kDa 
• Atom Count: 2,269 
• Modeled Residue Count: 283 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Mt-VDAC1 of Non-selective voltage-gated ion channel VDAC1	A [auth X]	295	Mus musculus	Mutation(s): 0  Gene Names: Vdac1, Vdac5 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PX4	C [auth X]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C36 H73 N O8 P CITHEXJVPOWHKC-UUWRZZSWSA-O
MPD	B [auth X]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.298 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.426	α = 90
b = 58.354	β = 98.17
c = 66.822	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-08 
Deposition Author(s): Lolicato, M., Arrigoni, C.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History  

• Version 1.0: 2025-01-08
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references