The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex

Structure. 2021 May 6;29(5):467-478.e6. doi: 10.1016/j.str.2020.12.006. Epub 2021 Jan 6.


In the non-homologous end-joining (NHEJ) of a DNA double-strand break, DNA ends are bound and protected by DNA-PK, which synapses across the break to tether the broken ends and initiate repair. There is little clarity surrounding the nature of the synaptic complex and the mechanism governing the transition to repair. We report an integrative structure of the synaptic complex at a precision of 13.5 Å, revealing a symmetric head-to-head arrangement with a large offset in the DNA ends and an extensive end-protection mechanism involving a previously uncharacterized plug domain. Hydrogen/deuterium exchange mass spectrometry identifies an allosteric pathway connecting DNA end-binding with the kinase domain that places DNA-PK under tension in the kinase-active state. We present a model for the transition from end-protection to repair, where the synaptic complex supports hierarchical processing of the ends and scaffold assembly, requiring displacement of the catalytic subunit and tension release through kinase activity.

Keywords: DNA repair; DNA-PK; crosslinking mass spectrometry; hydrogen/deuterium exchange; modeling; non-homologous end-joining; structure; synaptic complex.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • DNA End-Joining Repair
  • DNA-Activated Protein Kinase / chemistry*
  • DNA-Activated Protein Kinase / metabolism
  • HeLa Cells
  • Holoenzymes
  • Humans
  • Molecular Docking Simulation
  • Protein Binding
  • Synaptonemal Complex / chemistry*
  • Synaptonemal Complex / metabolism


  • Holoenzymes
  • DNA-Activated Protein Kinase