Fig. 4: Binding regions of cyt c2 and cyt cy on CIII2CIV.
The binding regions were defined by XL-MS-guided docking, and the subunits of CIII2CIV are colored as in Fig. 2 except the monomer B of CIII2 shown in light gray. Only the binding regions on monomer A are shown. a Cyt c2 (PDB: 1C2N) was docked onto CIII2 and CIV using PatchDock guided by DMTMM-generated XLs as distance restraints. This yielded one cluster of models on CIV and one per monomer of CIII2. b A model of cyt domain of cy, generated using P. denitrificans cyt c552 structure (PDB: 3M97) as a template (RMSD between template and model: 0.2 Å) was docked on CIII2 as in a, except that both DMTMM- and DSBU-generated XLs provided distance restraints. Two binding clusters for cyt domain of cy per monomer of CIII2 were found. The two clusters are located behind each other on a side view but are clearly visible on top views (Supplementary Fig. 4h–j, labeled 1 and 2). Only cluster 1 that is closer to cyt c1 and overlapping with the binding region of cyt c2 is shown. In all cases, ten representative models are shown to visualize the clusters of binding models. No binding region for cyt cy on CIV could be defined since no XL was found between the proteins.
