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. Author manuscript; available in PMC: 2019 Aug 13.
Published in final edited form as: Nature. 2017 Mar 1;544(7649):196–201. doi: 10.1038/nature21393

Extended Data Figure 7. Conserved conformation of Head, Middle, and Med14-Middle interface between Sp Mediator and Sp holoenzyme, and Mediator rearrangements upon holoenzyme formation.

Extended Data Figure 7.

a. The structure of the Head module is very similar in free Mediator (yellow) and holoenzyme (blue), except for the positions of the Med17N and Med6C portions, which connect to the knob and Med14, respectively. RMSD values between 1334 Cα atom pairs in corresponding portions of the Mediator and holoenzyme EM structures of the Head is 1.9 Å (the Med17N and Med14C domains that move with the knob were not included in the RMSD calculation). b, The structure of the Middle module is also very similar in free Mediator (yellow) and holoenzyme (blue). RMSD values between Cα 801 atom pairs in corresponding portions of the Mediator and holoenzyme EM structures of the Middle is 2.7 Å. c, Med14 has a considerable conformational change between free Mediator (yellow) and holoenzyme (blue). d, The structure of the Med14 (RM1)-Middle interface is the same in free Mediator and holoenzyme. e, Med14-interacting Med17N and Med6C move along with the top of Med14. f, Repositioning of the Middle upon holoenzyme formation closes the CTD-binding gap. It also brings Middle subunits Med4 and Med9 into contact with polymerase’s Rpb1 foot (highlighted in light green). The rigidity of the Middle module effectively links the contacts Mediator establishes with Rpb1’s CTD and foot domains. g, Sc core MED-ITC structure with Head, Middle, and Med14 portions colored in purple, blue, and green, respectively. h, Matching the Head portion of Sc core MED-ITC to the Head portion of the published cryo-EM map of free S cerevisiae Mediator1 (semi-transparent teal) shows a large rearrangement of the Middle upon Sc Mediator interaction with RNAPII. i, Matching the Head portion of Sc MED-PIC to the Head portion of the published cryo-EM map of free S cerevisiae Mediator1 (semi-transparent teal) also shows a large rearrangement of the Middle upon Sc Mediator interaction with RNAPII.