Figure 3. Cross-linking and Mass Spectrometry of the Med-PIC Complex
(A) Network diagram of cross-links between subunits of the Med-PIC complex (676 of the 1,642 total cross-links identified here). Subunits are coloredas in
Figure 1A and as indicated. Blue lines represent cross-links formed in the Med-PIC complex, including Gcn4 and TFIIS (total of 54 subunits). Green lines represent
cross-links formed in a Mediator-pol II complex (33 subunits). Cross-links formed in both complexes are indicated in black. Cross-links between polII subunits
and between pol II and TFIIB, -E, -F, -S and TBP are shown in the inset.
(B) Validation of cross-links. Top: scoring of matches (SVM confidence score) to the sequence database (target) and to a scrambled sequence database (decoy),
showing a 4% ‘‘false discovery rate’’ (percentage of decoy matches exceeding the acceptance threshold in this work [red line]). Bottom: validation against near
atomic structures; 397 of 1642 cross-links could be mapped to Ca-Cadistances in crystal structures of pol II (pdb:1wcm), Mediator Head module (pdb:4gwp), pol
II -TFIIB (pdb:4bbr), pol II-TFIIA-TBP (pdb:1rm1), Med7C/21 and Med7N/31 dimers (pdb:1yke, pdb:3fbi). Almost all (357, or 90%) of the mappable cross-links
were consistent with the 35 A ̊upper limit.
(C) Distribution of 1642 cross-links between the 13 proteins and subcomplexes defined by the color code in (A). The area of each bubble is proportional to the
number of cross-links found between the pair of proteins and subcomplexes indicated. See alsoFigure S3.
1414 Cell 166 , 1411–1422, September 8, 2016