Supplementary Figure 6: Overview and structural analysis of the DSS cross-linking mass spectrometry data.

(a) Two-dimensional visualization of all inter-protein DSS cross-links obtained for the SSU processome sample generated with xiNET⁵². Protein subunits are represented as spheres. The size of each sphere is proportional to the molecular weight of the corresponding protein. Subunits belonging to complexes or those forming a structural unit are highlighted with the same color. The thickness of the line connecting two subunits is proportional to the number of shared cross-links. All U-three-proteins (Utp) are labeled with their respective number. (b) Cross-links plotted onto the structure of the SSU processome shown as direct connection between the Cα of individual lysine residues. All Cα atoms found in the cross-linking analysis are shown as spheres and are colored according to Figure 1. In cases where two copies of a protein are present (Kre33, Emg1, and Nop1), the shorter cross-link is displayed. Conformational flexibility of the central domain and a reconstruction of this domain based on only a small subpopulation of the data (15%) may explain the high abundance of cross-links with longer distances in this region. These cross-links may result from other conformational states of the central domain. (c) Histogram of all Cα cross-link distances in Å. 87.2% of all cross-link distances are within 32 Å. (d) SDS-PAGE analysis of a purified SSU processome sample cross-linked with increasing concentrations of DSS. The gel region and DSS concentration used for mass spectrometry analysis experiments are highlighted in green.