Fig. 4: Binding structure of UV-DDB to CPD in the nucleosome.
From: Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome
a Residues contacting the CPD are indicated, and the interacting surface of DDB2 with the CPD (pink), the backbone phosphate of the damaged strand (orange), and the orphan bases of the undamaged strand (yellow) are highlighted. b Schematic representation of DDB2 binding to CPD in nucleosomes. c Close-up view of contacting residues of DDB2. Distances between CPD and DDB2 residues were measured by the Pymol software. Bending angle of DNA in the nucleosome at the SHL ± 2 position in the absence (d) or presence (e) of UV-DDB. DNA in the nucleosome without UV-DDB was obtained from the previously determined structural model (PDB ID: 3AFA). Bending angles were measured by generating helical axes of DNA with the 3DNA software53.
