2XA0 | pdb_00002xa0

Crystal structure of BCL-2 in complex with a BAX BH3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.242 (Depositor) 
  • R-Value Work: 
    0.222 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2XA0

This is version 1.3 of the entry. See complete history

Literature

Evidence that Inhibition of Bax Activation by Bcl- 2 Involves its Tight and Preferential Interaction with the Bh3 Domain of Bax.

Ku, B.Liang, C.Jung, J.U.Oh, B.H.

(2011) Cell Res 21: 627

  • DOI: https://doi.org/10.1038/cr.2010.149
  • Primary Citation Related Structures: 
    2XA0

  • PubMed Abstract: 

    Interactions between the BCL-2 family proteins determine the cell's fate to live or die. How they interact with each other to regulate apoptosis remains as an unsettled central issue. So far, the antiapoptotic BCL-2 proteins are thought to interact with BAX weakly, but the physiological significance of this interaction has been vague. Herein, we show that recombinant BCL-2 and BCL-w interact potently with a BCL-2 homology (BH) 3 domain-containing peptide derived from BAX, exhibiting the dissociation constants of 15 and 23 nM, respectively. To clarify the basis for this strong interaction, we determined the three-dimensional structure of a complex of BCL-2 with a BAX peptide spanning its BH3 domain. It revealed that their interactions extended beyond the canonical BH3 domain and involved three nonconserved charged residues of BAX. A novel BAX variant, containing the alanine substitution of these three residues, had greatly impaired affinity for BCL-2 and BCL-w, but was otherwise indistinguishable from wild-type BAX. Critically, the apoptotic activity of the BAX variant could not be restrained by BCL-2 and BCL-w, pointing that the observed tight interactions are critical for regulating BAX activation. We also comprehensively quantified the binding affinities between the three BCL-2 subfamily proteins. Collectively, the data show that due to the high affinity of BAX for BCL-2, BCL-w and A1, and of BAK for BCL-X(L), MCL-1 and A1, only a subset of BH3-only proteins, commonly including BIM, BID and PUMA, could be expected to free BAX or BAK from the antiapoptotic BCL-2 proteins to elicit apoptosis.


  • Organizational Affiliation
    • Department of Biological Sciences, KAIST Institute for the Biocentury, Daejeon, Korea.

Macromolecule Content 

  • Total Structure Weight: 52.87 kDa 
  • Atom Count: 2,733 
  • Modeled Residue Count: 326 
  • Deposited Residue Count: 476 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
APOPTOSIS REGULATOR BCL-2
A, B
207Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
PHAROS:  P10415
GTEx:  ENSG00000171791 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10415
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
APOPTOSIS REGULATOR BAX
C, D
31Mus musculusMutation(s): 0 
UniProt
Find proteins for Q07813 (Mus musculus)
Explore Q07813 
Go to UniProtKB:  Q07813
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07813
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.242 (Depositor) 
  • R-Value Work:  0.222 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.973α = 90
b = 81.973β = 90
c = 138.85γ = 120
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-05-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description