Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1

Genes Dev. 2015 Nov 15;29(22):2349-61. doi: 10.1101/gad.272278.115. Epub 2015 Nov 5.


The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 oligomerizes into a heptameric complex known as the apoptosome, which recruits and activates cell-killing caspases. Here we present an atomic structure of an intact mammalian apoptosome at 3.8 Å resolution, determined by single-particle, cryo-electron microscopy (cryo-EM). Structural analysis, together with structure-guided biochemical characterization, uncovered how cytochrome c releases the autoinhibition of Apaf-1 through specific interactions with the WD40 repeats. Structural comparison with autoinhibited Apaf-1 revealed how dATP binding triggers a set of conformational changes that results in the formation of the apoptosome. Together, these results constitute the molecular mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.

Keywords: Apaf-1; apoptosis; apoptosome; caspase activation; caspase-9; cryo-EM structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / metabolism*
  • Animals
  • Apoptosomes / chemistry*
  • Apoptotic Protease-Activating Factor 1 / metabolism*
  • Caspase 9 / metabolism
  • Cell Line
  • Cryoelectron Microscopy
  • Cytochromes c / genetics
  • Cytochromes c / metabolism*
  • Enzyme Activation / physiology
  • Humans
  • Models, Molecular*
  • Mutation / genetics
  • Protein Binding
  • Protein Structure, Tertiary


  • Apoptosomes
  • Apoptotic Protease-Activating Factor 1
  • Adenosine Triphosphate
  • Cytochromes c
  • Caspase 9