Fig. 2
Cross-linking of the CNPG complex. a Number of cross-linked peptides identified from the reaction of ArGO1-3 or BDG with the CNGP complex. The CNGP complex was treated with 1 mM cross-linker at RT for 1 h. The identified cross-links using four cross-linkers are provided in the source data file. b Annotated MS/MS spectrum of an ArGO1-linked peptide pair from the CNGP complex. The precursor charge and m/z are shown in the spectrum. The highest peak (in bold) in the middle is the precursor. c–f Rosetta docking of Nop10 to Cbf5 with DSS and ArGO1 distance restraints. c Cross-links identified between Nop10 and Cbf5 are mapped to the yeast CNG sub-complex structure (PDB code: 3U28). Between Nop10 and Cbf5, three K–K cross-links were identified with DSS (dotted yellow lines) and three R–R cross-links were identified with ArGO1 (dotted red lines). d Summary of Rosetta docking results with DSS or DSS+ ArGO1 distance restraints. Each dot represents a cluster of conformations thus obtained, with the cluster size (number of poses in a cluster) and ligand−RMSD (the distance between a representative pose of a cluster and the native structure) shown on the y- and x-axis, respectively. e Box plot showing the distribution of the RMSD values of top 200 conformers obtained from Rosetta docking. The median, the interquartile range, the minimum, and maximum values are indicated by line, box, and whiskers (n = 200). The RMSD values of top 200 conformers obtained with Rosetta 3.10 using distance restraints of DSS cross-links alone or those of DSS+ ArGO1 are provided in the source data file. f Representative structure of the largest conformational cluster obtained with DSS or DSS+ ArGO1 cross-links, superimposed with the native structure
