Extended Data Fig. 12: Application of the docking pipeline.

a–d, pre-TCRC modelling. a, PDB files of E. coli ECs were downloaded and prepared by extracting chains corresponding to RNAP subunits and NusA, then refined using YASARA Structure. E. coli UvrA was modelled using the homology template server I-TASSER. b, UvrA was docked to ECs using PatchDock, with the RNAP-UvrA cross-links as distance restraints. c, PDB coordinates file of E. coli UvrD in the apo form was trimmed to the first 640 residues and refined, then docked to the top EC-UvrA (as ranked by cross-link satisfaction) from the previous step. d, EC-UvrA-UvrD complexes generated in the previous step were ranked by RNAP–UvrD cross-link satisfaction and used as receptors to dock UvrD CTD. Results were clustered using ProFit (v.3.1), and finally analysed for the UvrAD DNA-binding regions alignment with the DNA path in the EC. e–g, TCRC modelling. e, Same as a. Docking was repeated using EC-UvrA1 complexes as receptors and additional UvrA-UvrA distance restraints to generate EC-UvrA12 complexes. f, Same as (c). Structure then docked to the top EC-UvrA12 complexes generated in the previous step, as ranked by RNAP-UvrA and UvrA-UvrA cross-link satisfaction. g, Top EC-UvrA12-UvrD complexes generated in the previous step were divided into two groups based on the docked UvrD model (apo vs. closed), and used as input to the dimer-assembly component (Extended Data Fig. 11 and Methods). UvrD poses from the two groups were cross-matched to generate EC-UvrA12-UvrD12 complexes, analysed for UvrD-UvrD cross-link satisfaction and steric clashes, and used as receptors to dock UvrD1 CTD. Results were clustered using ProFit (v.3.1) and analysed for agreement with UvrA-dimer structures and alignment of Uvr DNA-binding regions with the DNA path in the EC. Final complexes were refined with YASARA Structure and re-analysed with Jwalk for cross-link satisfaction.