Extended Data Fig. 5: Mapping of cross-links onto Pol II-SPT6-Elongin model.

a. Frequency distribution of the Cα-Cα distances between BS3-cross-linked residues. The number of unique cross-links is plotted against the Euclidean distance between Cα atoms of the two cross-linked residues. The histogram shows number of cross-links that falls into a distance range bin (3-6 Å, 6–9 Å, ect.). 30 Å is the maximum distance possible between Cα atoms of BS3-cross-linked Lys pairs in fully stretched conformation. In blue are the bins that satisfy a distance criterium of <30 Å, in red are those that violate it. b. Mapping of cross-links onto the Pol II-SPT6-Elongin structure (structure 1), corresponding to the plot in panel a. Cross-links are shown as solid lines and color coded is in a. c. Close-up view of the cross-links between ELOA C-terminal linker (magenta) and Pol II protrusion (grey). There are 91 cross-linked peptide spectrum matches (CSMs) of the ELOA K688-RPB2 K223 cross-link, 15 CSMs of the ELOA K697-RPB2 K223 cross-link and 41 CSMs of the ELOA K697-RPB2 K228 cross-link. d. Close-up view of the cross-link between ELOA latch (magenta) and Pol II funnel helices (grey). There are 4 CSMs of the ELOA K559-RPB1 K707 cross-link. e, f. Cross-linking sites of ELOA TND on Pol II surface, front view (e) and back view (f). The Pol II lysine residues that cross-link to ELOA TND are shown as spheres. g, h. Superposition of the Pol II-DSIF structure (PDB: 5OIK⁵²) onto the Pol II-SPT6-Elongin structure, front view (g) and back view (h). The Pol II lysine residues that cross-link to ELOA TND are shown as spheres. See cross-links in Supplementary Data 1.