Dimers of DNA-PK create a stage for DNA double-strand break repair

Structure of the human SAGA coactivator complex: The divergent architecture of human SAGA allows modular coordination of transcription activation and co-transcriptional splicing

“…The characteristic TRRAP module has a tripartite HEAT repeat organization, consisting of a central N-terminal repeat and a circular cradle, followed by a FAT (Focal adhesion kinase targeting) domain and a PI3K that connects to the core module (Fig. 1E, S5) and is embedded in the HEAT repeats, as also found in ySAGA, yeast NuA4 and its metazoan counterpart Tip60 (15,16,31), and in active kinases such as mTOR (32,33), DNA-PKcs (34), and ATM (35) (Fig. S8A-E).…”

The Multifaceted Roles of Ku70/80

“…This suggests a limited dynamic of these loops that are not engaged in crystal contacts ( Figure 3 a). In recent crystal and cryoEM structures of the Ku-DNA complex bound with DNA-PKcs or peptides [ 10 , 11 , 26 ], these loops also adopt the same conformation, suggesting a stable conformation of these loops with or without DNA. It remains to be documented if some rearrangements can happen during Ku translocation or if Ku threads in a helical manner like a screw on a nut.…”

“…Briefly, recent structural studies characterized interaction sites of Ku with c-NHEJ proteins. The structure of the DNA-PK, formed by Ku and DNA-PKcs, was determined by cryo-electron microscopy (cryoEM) by several groups (for example, [ 10 , 11 ]). Recently, Chaplin et al identified particles corresponding to a dimer of DNA-PK holoenzymes that reconstitute a synapse of DNA ends.…”

“…This dimer is mediated by a domain swap mechanism of the conserved C -terminal helix of Ku80. In this dimer, DNA ends present in each DNA-PK run almost parallel [ 11 ]. Ku can also recruit, at DSBs, several c-NHEJ factors containing motifs called Ku-binding motifs (KBMs) [ 12 , 13 ].…”

A Personal History of Using Crystals and Crystallography to Understand Biology and Advanced Drug Discovery

“…Our own laboratory has been impacted by this revolution. As described in the previous section, the structure of the very large enzyme DNA-PKcs was solved by the X-ray analysis at 4.3 Å [98], but recently, structures have been obtained of DNA-PKcs by cryo-EM at 2.8 Å and its complex with Ku70/80 and DNA at 3.8 Å resolution (previously 6.6 Å) [111], examples of how the resolution revolution has changed structural biology over the past decade. It has even allowed Harren Jhoti and Pamela Williams and the team at Astex along with collaborators at Isohelio Ltd, to develop fragment-based drug discovery using cryo-EM, demonstrating that fragment-sized molecules can be accurately described when bound to large proteins, allowing cryo-EM to contribute even further to drug discovery [112]).…”