5VWX

Bak core latch dimer in complex with Bim-h0-h3Glt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.4 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2 homologous antagonist/killer
A, C
170Homo sapiensMutation(s): 1 
Gene Names: BAK1BAKBCL2L7CDN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens)
Explore Q16611 
Go to UniProtKB:  Q16611
PHAROS:  Q16611
GTEx:  ENSG00000030110 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16611
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2-like protein 11
B, D
23Homo sapiensMutation(s): 6 
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens)
Explore O43521 
Go to UniProtKB:  O43521
PHAROS:  O43521
GTEx:  ENSG00000153094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43521
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.629α = 90
b = 76.481β = 90
c = 77.546γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaG3046
National Health and Medical Research Council (NHMRC, Australia)AustraliaG2564
National Health and Medical Research Council (NHMRC, Australia)AustraliaG2754

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: 2017-12-06
    Changes: Author supporting evidence
  • Version 1.3: 2018-04-18
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence, Derived calculations, Structure summary