Fig. 4: Conformational reorganisation of XPF–ERCC1 engaged by a DNA-junction substrate. | Nature Communications

Fig. 4: Conformational reorganisation of XPF–ERCC1 engaged by a DNA-junction substrate.

From: Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation

Fig. 4

a Two orthogonal views of DNA-bound XPF–ERCC1 ribbon structure coloured by domain according to Fig. 1a. The dsDNA duplex is shown in purple. The ribbon model is shown with the cryo-EM composite map, ranging from 5.9–7.7 Å global resolution. b Top and middle: two orthogonal views comparing segmented DNA-free and DNA-bound maps. The DNA-bound map displayed is the globally refined and unsharpened 7.7 Å map. The DNA-free map displayed is the globally refined and unsharpened 4.0 Å map low-pass filtered to 9 Å resolution to display comparable levels of detail to the DNA-bound map. Both maps were segmented in UCSF Chimera revealing sub-volumes for the XPF HLM (pink), XPF nuclease–ERCC1 NLD dimer (blue), 2×(HhH)2 domain (yellow) and dsDNA (white). Bottom: two orthogonal views of the HLM and the CM/ERCC1 dsDNA-binding module. Each sub-volume contains the ribbon model of DNA-bound XPF–ERCC1, orange dotted line indicates unmodeled density corresponding to the position of the first RecA2 domain flexible insert. c Fitted model for the dimeric 2×(HhH)2 domain engaging dsDNA via the minor groove, placed within map density. Major groove distance and dsDNA-binding residues are indicated. The dsDNA-binding hairpin residues of ERCC1 are highlighted in yellow. d Model for the XPF RecA1–nuclease/ERCC1 NLD interface following substrate engagement. Labels and red circles indicate the XPF active site location. e Human XPF nuclease–ERCC1 NLD dimer, 2×(HhH)2 domain and dsDNA positioned within the cryo-EM map together with a structurally superposed A. pernix XPF structure (PDB code 2BGW) bound to dsDNA. A similar dsDNA trajectory is evident (purple box). f 2D class averages of DNA-bound XPF–ERCC1 with coloured dotted lines indicating the position of domains according to the key. g Comparison of 2D classes of the same molecular views from DNA-free (left column) and DNA-bound (right column) XPF–ERCC1 with coloured circles indicating the position of key domains, coloured according to panel (f).

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