Fig. 2: The XPG nuclease bridges the opposing ends of the NER bubble, providing an unexpected 5′ incision sensing mechanism.

a View of XPG at the 3′ DNA junction. XPG is depicted as cartoon and transparent surface and colored in dark green. The path of the DNA through TFIIH’s XPD subunit is shown by black spheres placed at the phosphorus atoms. b Crosslinks between XPG and XPD mapped onto the PInC structure. The XPD Arch and Fe-S domains are colored in orange and purple, respectively. XPG and XPD residues participating in the crosslinks are depicted as blue and black spheres, respectively. A schematic of the crosslinks mapped onto XPD’s and XPG’s sequences is shown above. Conserved structural motifs in the XPG catalytic core are shown; the two XPG coiled-coil helices are shown in purple; the XPG anchor domain is shown in gray. c The XPG anchor domain fitted into a segment from the TFIIH/XPA/DNA cryo-EM density (EMDB accession code: EMD–4970). d Overlay of AlphaFold2 docking models of the XPG-anchor and the p62 XPD-anchor with XPD. The β-hairpin, packed against the XPG-anchor domain is highlighted by a green circle. The acidic patch of XPG is highlighted in orange. The inset displays the sequence alignment of the acidic patches of human XPG and XPC. e Zoomed-in view of the β-hairpin interacting with the XPD anchor and ssDNA at the 5′ junction. A hydrophobic cluster involving residue I290 colored in green. I290N substitution is a recognized XP/CS disease mutant. f A CPD lesion blocked inside XPD’s DNA-binding groove near His135 and 8 nucleotides away from the 3′ junction.