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, Kyung Jong Lee, Jian Shi, David J. Chen, Phoebe L. Stewart

Research output: Contribution to journalArticle

61 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)468-477
Number of pages10
JournalStructure
Volume16
Issue number3
DOIs
StatePublished - Mar 11 2008

Keywords

  • DNA
  • SIGNALING

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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