Cryo-EM Structure of the DNA-Dependent Protein Kinase Catalytic Subunit at Subnanometer Resolution Reveals α Helices and Insight into DNA Binding
Dewight R. Williams,1 Kyung-Jong Lee,2 Jian Shi,1 David J. Chen,2 and Phoebe L. Stewart1,

1 Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
2 Molecular Radiation Biology Division, Department of Radiation Oncology, UT Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA

Corresponding author
Phoebe L. Stewart
phoebe.stewart@vanderbilt.edu

Summary
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) regulates the nonhomologous end joining pathway for repair of double-stranded DNA (dsDNA) breaks. Here, we present a 7Å resolution structure of DNA-PKcs determined by cryo-electron microscopy single-particle reconstruction. This structure is composed of density rods throughout the molecule that are indicative of α helices and reveals structural features not observed in lower resolution EM structures. Docking of homology models into the DNA-PKcs structure demonstrates that up to eight helical HEAT repeat motifs fit well within the density. Surprisingly, models for the kinase domain can be docked into either the crown or base of the molecule at this resolution, although real space refinement suggests that the base location is the best fit. We propose a model for the interaction of DNA with DNA-PKcs in which one turn of dsDNA enters the central channel and interacts with a resolved α-helical protrusion.

3月11日《结构》（Structure）杂志封面的图片背景是一个DNA依赖型的蛋白激酶分子（DNA-PKcs）的冷冻电镜图，而前景则为该图描绘出的亚纳米级的DNA依赖型的蛋白激酶分子。DNA双链断裂被公认为由DNA依赖型的蛋白激酶决定，DNA依赖型蛋白激酶的催化亚基是通过调节非同源末端连接通路来修复DNA的双链断链的。