Bak BH3-in-Groove dimer (GFP)

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Bak Core and Latch Domains Separate during Activation, and Freed Core Domains Form Symmetric Homodimers.

Brouwer, J.M.Westphal, D.Dewson, G.Robin, A.Y.Uren, R.T.Bartolo, R.Thompson, G.V.Colman, P.M.Kluck, R.M.Czabotar, P.E.

(2014) Mol Cell 55: 938-946

  • DOI: https://doi.org/10.1016/j.molcel.2014.07.016
  • Primary Citation of Related Structures:  
    4U2U, 4U2V

  • PubMed Abstract: 

    Apoptotic stimuli activate and oligomerize the proapoptotic proteins Bak and Bax, resulting in mitochondrial outer-membrane permeabilization and subsequent cell death. This activation can occur when certain BH3-only proteins interact directly with Bak and Bax. Recently published crystal structures reveal that Bax separates into core and latch domains in response to BH3 peptides. The distinguishing characteristics of BH3 peptides capable of directly activating Bax were also elucidated. Here we identify specific BH3 peptides capable of "unlatching" Bak and describe structural insights into Bak activation and oligomerization. Crystal structures and crosslinking experiments demonstrate that Bak undergoes a conformational change similar to that of Bax upon activation. A structure of the Bak core domain dimer provides a high-resolution image of this key intermediate in the pore-forming oligomer. Our results confirm an analogous mechanism for activation and dimerization of Bak and Bax in response to certain BH3 peptides.

  • Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,Bcl-2 homologous antagonist/killerA [auth B],
B [auth D],
D [auth A]
313Aequorea victoriaHomo sapiens
This entity is chimeric
Mutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
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 GroupsP42212Q16611
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CR2
A [auth B],
B [auth D],
D [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.19α = 90
b = 63.84β = 98.35
c = 122.02γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1059331
National Health and Medical Research Council (NHMRC, Australia)Australia1023055
National Health and Medical Research Council (NHMRC, Australia)Australia1016701

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection