Supplementary Figure 7: Euclidean Cα-Cα distances of the cross-links on the crystal structures PDB 4IFD and PDB 2WP8 and a representative high-resolution MS/MS cross-link spectrum.
From: A strategy for dissecting the architectures of native macromolecular assemblies
a) Euclidean Cα-Cα distances of the cross-links on the crystal structures PDB 4IFD and PDB 2WP8. The blue bars represent the cross-link distances measured on the 4IFD structure, and the pink bar represents the cross-link distances measured on the 2WP8 structure. Asterisks indicate the cross-links that are longer than 44 Å. b) A high-resolution MS/MS spectrum of the DSS cross-link between lysine 497 of Rrp44 and lysine 292 of Rrp45. The Cα-Cα distance between the cross-linked residues is 60.6 Å on the crystal structure. A ladder of HCD fragmentations occurs along the peptide bonds of both peptide chains, and fragmentations are labeled as b-ions and y-ions. The underlined methionine residue is oxidized. The charge state of this peptide ion is +5. The asterisk designates an immonium ion, which is commonly observed in HCD fragmentation spectra.
