SAP domain forms a flexible part of DNA aperture in Ku70/80

FEBS J. 2021 Jul;288(14):4382-4393. doi: 10.1111/febs.15732. Epub 2021 Feb 16.


Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double-strand DNA breaks to maintain genomic integrity during the entire cell cycle. The Ku70/80 complex recognizes DNA breaks and serves as an essential hub for recruitment of NHEJ components. Here, we describe intramolecular interactions of the Ku70 C-terminal domain, known as the SAP domain. Using single-particle cryo-electron microscopy, mass spectrometric analysis of intermolecular cross-linking and molecular modelling simulations, we captured variable positions of the SAP domain depending on DNA binding. The first position was localized at the DNA aperture in the Ku70/80 apo form but was not observed in the DNA-bound state. The second position, which was observed in both apo and DNA-bound states, was found below the DNA aperture, close to the helical arm of Ku70. The localization of the SAP domain in the DNA aperture suggests a function as a flexible entry gate for broken DNA. DATABASES: EM maps have been deposited in EMDB (EMD-11933). Coordinates have been deposited in Protein Data Bank (PDB 7AXZ). Other data are available from corresponding authors upon a request.

Keywords: DNA double-strand break; Ku70/80; SAP domain; integrative structural biology; nonhomologous end joining.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • DNA Breaks, Double-Stranded*
  • DNA End-Joining Repair*
  • Humans
  • Ku Autoantigen / chemistry*
  • Protein Conformation
  • Protein Domains


  • DNA
  • Ku Autoantigen