8EJA | pdb_00008eja

Computational design of potent and selective inhibitors of Bak and Bax

• PDB DOI: https://doi.org/10.2210/pdb8EJA/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-16 Released: 2024-03-20 
• Deposition Author(s): Bera, A.K., Berger, S.A., Baker, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.264 (Depositor) 

Literature

Computational design of potent and selective binders of BAK and BAX.

Berger, S., Lee, E.F., Harris, T.J., Tran, S., Bera, A.K., Arguinchona, L., Kang, A., Sankaran, B., Kasapgil, S., Miller, M.S., Smyth, S., Lutfi, M., Uren, R.T., Kluck, R.M., Colman, P.M., Fairlie, W.D., Czabotar, P.E., Baker, D., Birkinshaw, R.W.

(2025) Sci Adv 11: eadt4170-eadt4170

• PubMed: 40911686 
• DOI: https://doi.org/10.1126/sciadv.adt4170
• Primary Citation of Related Structures:  
  8EJA, 9CLB


• PubMed Abstract: 
  

  Potent and selective binders of the key proapoptotic proteins BAK and BAX have not been described. We use computational protein design to generate high affinity binders of BAK and BAX with greater than 100-fold specificity for their target. Both binders activate their targets when at low concentration, driving pore formation, but inhibit membrane permeabilization when in excess. Crystallography shows that the BAK binder induces BAK unfolding, exposing the α6 helix and BH3 domain. Together, these data suggest that upon binding, BAK or BAX unfold; at high binder concentrations, self-association of the partially folded BAK or BAX proteins is blocked and the membrane remains intact, whereas at low concentrations, dimers form, and the membrane ruptures. Our designed binders modulate apoptosis via direct, specific interactions with BAK and BAX and reveal that for therapeutic strategies targeting BAK and BAX, inhibition requires saturating binder concentrations at the site of action.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, VIC 3086, Australia.
Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia.
School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia.
Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.
Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3052, Australia.
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.62 kDa 
• Atom Count: 1,881 
• Modeled Residue Count: 225 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aBAK	A [auth B], B [auth A]	118	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.829	α = 90
b = 53.829	β = 90
c = 206.038	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Bera, A.K., Berger, S.A., Baker, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release
  
• Version 1.1: 2025-10-01
  Changes: Database references, Structure summary