9HPS | pdb_00009hps

Human BclxLdeltaLT-VDAC1-N fusion protein complex structure

• PDB DOI: https://doi.org/10.2210/pdb9HPS/pdb

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


• Deposited: 2024-12-16 Released: 2025-09-17 
• Deposition Author(s): Janowski, R., Niessing, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structural basis of apoptosis induction by the mitochondrial voltage-dependent anion channel.

Daniilidis, M., Gunsel, U., Broutzakis, G., Leitl, K.D., Janowski, R., Fredriksson, K., Niessing, D., Gatsogiannis, C., Hagn, F.

(2025) Nat Commun 16: 9481-9481

• PubMed: 41145501 
• DOI: https://doi.org/10.1038/s41467-025-65363-1
• Primary Citation Related Structures: 
  9HPS


• PubMed Abstract: 
  

  The voltage-dependent anion channel (VDAC) is the main gateway for metabolites across the mitochondrial outer membrane. VDAC oligomers are connected to apoptosis induced by various stimuli. However, the mechanistic and structural basis of apoptosis induction by VDAC remains poorly understood. Here, using cryo-EM and NMR we show that VDAC1 oligomerization or confinement in small lipid nanodiscs triggers the exposure of its N-terminal α-helix (VDAC1-N) which becomes available for partner protein binding. NMR and X-ray crystallography data show that VDAC1-N forms a complex with the BH3 binding groove of the anti-apoptotic Bcl2 protein BclxL. Biochemical assays demonstrate that VDAC1-N exhibits a pro-apoptotic function by promoting pore formation of the executor Bcl2 protein Bak via neutralization of BclxL. This mechanism is reminiscent of BH3-only sensitizer Bcl2 proteins that are efficient inducers of Bax/Bak-mediated mitochondrial outer membrane permeabilization and ultimately apoptosis. The VDAC pathway most likely responds to mitochondrial stress or damage.

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Organizational Affiliation: 
• Structural Membrane Biochemistry and Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany.
Molecular Targets and Therapeutics Center (MTTC), Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany.
Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms Universität Münster, Münster, Germany.
AGC Biologics, Copenhagen, Denmark.
Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany.
Structural Membrane Biochemistry and Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany. [e-mail].
Molecular Targets and Therapeutics Center (MTTC), Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.01 kDa 
• Atom Count: 1,437 
• Modeled Residue Count: 164 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BclxLdeltaLT	A, B	207	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.12	α = 90
b = 98.75	β = 90
c = 103.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Janowski, R., Niessing, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release
  
• Version 1.1: 2025-11-05
  Changes: Database references