Structure of the apoptotic protease-activating factor 1 bound to ADP

Nature. 2005 Apr 14;434(7035):926-33. doi: 10.1038/nature03465.


Apoptosis is executed by caspases, which undergo proteolytic activation in response to cell death stimuli. The apoptotic protease-activating factor 1 (Apaf-1) controls caspase activation downstream of mitochondria. During apoptosis, Apaf-1 binds to cytochrome c and in the presence of ATP/dATP forms an apoptosome, leading to the recruitment and activation of the initiator caspase, caspase-9 (ref. 2). The mechanisms underlying Apaf-1 function are largely unknown. Here we report the 2.2-A crystal structure of an ADP-bound, WD40-deleted Apaf-1, which reveals the molecular mechanism by which Apaf-1 exists in an inactive state before ATP binding. The amino-terminal caspase recruitment domain packs against a three-layered alpha/beta fold, a short helical motif and a winged-helix domain, resulting in the burial of the caspase-9-binding interface. The deeply buried ADP molecule serves as an organizing centre to strengthen interactions between these four adjoining domains, thus locking Apaf-1 in an inactive conformation. Apaf-1 binds to and hydrolyses ATP/dATP and their analogues. The binding and hydrolysis of nucleotides seem to drive conformational changes that are essential for the formation of the apoptosome and the activation of caspase-9.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Diphosphate / metabolism*
  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism
  • Adenosine Triphosphate / metabolism
  • Amino Acid Motifs
  • Apoptosis
  • Apoptotic Protease-Activating Factor 1
  • Binding Sites
  • Caspase 9
  • Caspases / metabolism
  • Crystallography, X-Ray
  • Cytochromes c / metabolism
  • Enzyme Activation
  • Hydrolysis
  • Models, Biological
  • Models, Molecular
  • Protein Binding
  • Protein Folding
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism*
  • Sequence Deletion / genetics
  • Structure-Activity Relationship


  • Apoptotic Protease-Activating Factor 1
  • Proteins
  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • Cytochromes c
  • Caspase 9
  • Caspases
  • Adenosine Triphosphatases