9PFZ | pdb_00009pfz

Architecture of human Voltage Dependent Anion Channel 1 in nanodiscs

• PDB DOI: https://doi.org/10.2210/pdb9PFZ/pdb
• EM Map EMD-71616: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-07 Released: 2026-05-27 
• Deposition Author(s): Modaresi, S.M., Degen, M., Hiller, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Small Molecule Inhibition of VDAC1 Reroutes Mitochondrial Metabolite Flux.

Modaresi, S.M., Zhang, L., Saei, A.A., Degen, M., Khavani, M., Gharibi, H., Vegvari, A., Ye, Z., Zhang, J., Pavlov, E., Jonas, E.A., Tew, K.D., Hiller, S., Townsend, D.M., Maldonado, E.N.

(2026) Mol Cells : 100369-100369

• PubMed: 42134653 
• DOI: https://doi.org/10.1016/j.mocell.2026.100369
• Primary Citation Related Structures: 
  9PFZ


• PubMed Abstract: 
  

  Voltage dependent anion channels (VDACs 1, 2 and 3) in the outer mitochondrial membrane control the flux of anions and oxidizable substrates that sustain mitochondrial metabolism. NADH closes VDAC by binding to a pocket, conserved in all isoforms, located in the inner wall of the channel. Previously, we identified the small molecule SC18 that targets the NADH-binding pocket of VDAC1 employing computational analysis. Here, we explored the interaction between SC18 and VDAC1 using High-resolution Nuclear Magnetic Resonance spectroscopy and Molecular Dynamics simulations. Atomically resolved data precisely confirmed the computational results, showing that SC18 binds to a site on VDAC1 that partially overlaps with the NADH binding pocket. SC18, in the presence of NADH blocked the conductance of VDAC1 reconstituted in lipid bilayers. To determine the metabolic effect of SC18, we combined readouts of mitochondrial metabolism and glycolysis with functional metabolomics and proteomics. Short-term treatment with SC18 inhibited mitochondrial metabolism and ATP production. Treatment over 24 h and 48 h further reduced mitochondrial uptake of pyruvate and glutamine, utilization of tricarboxylic acid cycle intermediates, as well as lipid, DNA and amino acid synthesis. Concomitant with the inhibition of mitochondrial metabolism, cellular uptake of glucose and glutamine increased in parallel with augmented lactate release. These results indicate that compensatory enhanced glycolysis sustains ATP production after impaired mitochondrial function induced by SC18 blockage of VDAC1. Our work set a mechanistic foundation for VDAC1 inhibition as a novel strategy to target and reprogram cancer metabolism through modulation of the biosynthetic ability of mitochondria.

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Organizational Affiliation: 
• Biozentrum, University of Basel, Basel, Switzerland.
Department of Pharmacology & Immunology, Medical University of South Carolina, Charleston, SC, USA.
Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, Berkeley, CA, USA.
Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Department of Molecular Pathobiology, New York University, New York, NY, USA.
Department of Internal Medicine (Endocrinology) and Neuroscience, Yale University, New Haven, CT, USA.
Department of Drug Discovery & Biomedical Sciences Medical University of South Carolina, Charleston, SC, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA. Electronic address: [e-mail].
Department of Drug Discovery & Biomedical Sciences Medical University of South Carolina, Charleston, SC, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 30.81 kDa 
• Atom Count: 2,171 
• Modeled Residue Count: 283 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-selective voltage-gated ion channel VDAC1	A	283	Homo sapiens	Mutation(s): 0  Gene Names: VDAC1, VDAC
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: ELECTRON MICROSCOPY
• Resolution: 5.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	UCSF ChimeraX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Modaresi, S.M., Degen, M., Hiller, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release