5JSN | pdb_00005jsn

Bcl2-inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb5JSN/pdb

• Classification: Viral Protein/Inhibitor
• Organism(s): Homo sapiens, unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-09 Released: 2016-11-16 
• Deposition Author(s): Shen, B.W., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer.

Berger, S., Procko, E., Margineantu, D., Lee, E.F., Shen, B.W., Zelter, A., Silva, D.A., Chawla, K., Herold, M.J., Garnier, J.M., Johnson, R., MacCoss, M.J., Lessene, G., Davis, T.N., Stayton, P.S., Stoddard, B.L., Fairlie, W.D., Hockenbery, D.M., Baker, D.

(2016) Elife 5

• PubMed: 27805565 
• DOI: https://doi.org/10.7554/eLife.20352
• Primary Citation Related Structures: 
  5JSB, 5JSN


• PubMed Abstract: 
  

  Many cancers overexpress one or more of the six human pro-survival BCL2 family proteins to evade apoptosis. To determine which BCL2 protein or proteins block apoptosis in different cancers, we computationally designed three-helix bundle protein inhibitors specific for each BCL2 pro-survival protein. Following in vitro optimization, each inhibitor binds its target with high picomolar to low nanomolar affinity and at least 300-fold specificity. Expression of the designed inhibitors in human cancer cell lines revealed unique dependencies on BCL2 proteins for survival which could not be inferred from other BCL2 profiling methods. Our results show that designed inhibitors can be generated for each member of a closely-knit protein family to probe the importance of specific protein-protein interactions in complex biological processes.

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Organizational Affiliation: 
• Department of Bioengineering, University of Washington, Seattle, United States.
Department of Biochemistry, University of Washington, Seattle, United States.
Department of Biochemistry, University of Illinois, Urbana, United States.
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
Department of Chemistry and Physics, LaTrobe Institute for Molecular Science, Melbourne, Australia.
Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Australia.
School of Cancer Medicine, La Trobe University, Melbourne, Australia.
The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
Department of Medical Biology, University of Melbourne, Parkville, Australia.
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
Institute for Protein Design, University of Washington, Seattle, United States.
Department of Genome Sciences, University of Washington, Seattle, United States.
Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia.
Howard Hughes Medical Institute, University of Washington, Seattle, United States.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.58 kDa 
• Atom Count: 4,540 
• Modeled Residue Count: 528 
• Deposited Residue Count: 666 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-2	A, C	215	Homo sapiens	Mutation(s): 0  Gene Names: BCL2
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl2 inhibitor	B, D	118	unidentified	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.005	α = 90
b = 65.005	β = 90
c = 134.314	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Shen, B.W., Stoddard, B.L.

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description