5VWY

Bak core latch dimer in complex with Bim-h3Pc-RT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design.

Brouwer, J.M., Lan, P., Cowan, A.D., Bernardini, J.P., Birkinshaw, R.W., van Delft, M.F., Sleebs, B.E., Robin, A.Y., Wardak, A., Tan, I.K., Reljic, B., Lee, E.F., Fairlie, W.D., Call, M.J., Smith, B.J., Dewson, G., Lessene, G., Colman, P.M., Czabotar, P.E.

(2017) Mol Cell 68: 659-672.e9

  • DOI: https://doi.org/10.1016/j.molcel.2017.11.001
  • Primary Citation of Related Structures:  
    5VWV, 5VWW, 5VWX, 5VWY, 5VWZ, 5VX0, 5VX1, 5VX2, 5VX3

  • PubMed Abstract: 

    • Certain BH3-only proteins transiently bind and activate Bak and Bax, initiating their oligomerization and the permeabilization of the mitochondrial outer membrane, a pivotal step in the mitochondrial pathway to apoptosis. Here we describe the first crystal structures of an activator BH3 peptide bound to Bak and illustrate their use in the design of BH3 derivatives capable of inhibiting human Bak on mitochondria ...

    Certain BH3-only proteins transiently bind and activate Bak and Bax, initiating their oligomerization and the permeabilization of the mitochondrial outer membrane, a pivotal step in the mitochondrial pathway to apoptosis. Here we describe the first crystal structures of an activator BH3 peptide bound to Bak and illustrate their use in the design of BH3 derivatives capable of inhibiting human Bak on mitochondria. These BH3 derivatives compete for the activation site at the canonical groove, are the first engineered inhibitors of Bak activation, and support the role of key conformational transitions associated with Bak activation.

    Organizational Affiliation: 

    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. Electronic address: czabotar@wehi.edu.au.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2 homologous antagonist/killerA170Homo sapiensMutation(s): 1 
Gene Names: BAK1, BAK, BCL2L7, CDN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens)
Explore Q16611 
Go to UniProtKB:  Q16611
PHAROS:  Q16611
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16611
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-like protein 11B26Homo sapiensMutation(s): 2 
Gene Names: BCL2L11, BIM
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens)
Explore O43521 
Go to UniProtKB:  O43521
PHAROS:  O43521
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43521
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.89α = 90
b = 37.54β = 107.86
c = 69.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
XDSdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1079706
National Health and Medical Research Council (NHMRC, Australia)Australia1058331
National Health and Medical Research Council (NHMRC, Australia)Australia1113133

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence