Fig. 3.

Formation of dumbbell DNA-PKcs-DNA dimers

A) P(r) functions for DNA-PKcs - 40bp DNA (blue), 40bp H-DNA (red) and 40bp Y-DNA (green) with the ratio 2:1 (DNA-PKcs :DNA), calculated from the experimental SAXS shown in the panel B. The light-colored P(r) functions are shown for the samples with equimolar DNA-PKcs:DNA molar ratio. The left panel shows cartoon representations of the atomistic models and its weights for each DNA-PKcs-DNA complex that were used to match the SAXS data shown in the panel B.

B) Experimental (black) and theoretical SAXS profiles for the single (cyan) and multistate-model of DNA-PKcs in the complex with 40bp DNA (blue), 40bp H-DNA (red) and 40bp Y-DNA (green) with the DNA-PKcs:DNA ratio 2:1. SAXS fits are shown together with the fit residuals and goodness of fit values (χ²). Guinier plots for experimental SAXS curves are shown in the inset.

C) Two atomistic models of DNA-PKcs dimer (model 1 and model 2) bridged by 40bpDNA(red). Model 2 was built based on the DNA-PK cryo-EM structure [15] by replacing KU with the DNA-PKcs. Model 1 was built by replacing both DNA-PKcs with DNA-PKcs-crystal structure [3]. Conformational variability in the N-HEAT 1–380 region as seen between DNA-PKcs from DNA-PK (PDBID 5Y3R) and DNA-PKcs crystal structure (PDBID: 5LUQ) results in altering of DNA-PKcs tilt. The N-HEAT 1–380, M-HEAT, FAT and kinase regions are colored as indicated. cryo-EM map for putative DNA-PKcs-DNA-KU complex [57] is shown in the bottom panel.