Core Mediator structure at 3.4 Å extends model of transcription initiation complex

The 3.4 Å crystal structure of the 15-subunit core Mediator complex in yeast. How Mediator triggers transcription The multiprotein Mediator complex has an essential role in regulating RNA polymerase II (Pol II) transcription in eukaryotes. Here, Patrick Cramer and colleagues report a 3.4 Å crystal structure of the 15-subunit core Mediator complex in yeast. They combine this with a previously determined cryo-EM structure of the Pol II pre-initiation complex to obtain an atomic model of Mediator bound to the pre-initiation complex. This model allows insights into the interactions of the head and middle modules of Mediator and provides a framework for understanding how Mediator stimulates Pol II C-terminal domain phosphorylation by TFIIH, a process which triggers productive transcription. Mediator is a multiprotein co-activator that binds the transcription pre-initiation complex (PIC) and regulates RNA polymerase (Pol) II 1 , 2 , 3 . The Mediator head and middle modules form the essential core Mediator (cMed) 4 , 5 , 6 , whereas the tail and kinase modules play regulatory roles 7 . The architecture of Mediator 5 , 8 , 9 , 10 and its position on the PIC 5 are known, but atomic details are limited to Mediator subcomplexes 11 , 12 . Here we report the crystal structure of the 15-subunit cMed from Schizosaccharomyces pombe at 3.4 Å resolution. The structure shows an unaltered head module 13 , 14 , 15 , and reveals the intricate middle module, which we show is globally required for transcription. Sites of known Mediator mutations cluster at the interface between the head and middle modules, and in terminal regions of the head subunits Med6 (ref. 16 ) and Med17 (ref. 17 ) that tether the middle module. The structure led to a model for Saccharomyces cerevisiae cMed that could be combined 5 with the 3.6 Å cryo-electron microscopy structure of the core PIC (cPIC) 18 . The resulting atomic model of the cPIC–cMed complex informs on interactions of the submodules forming the middle module, called beam, knob, plank, connector, and hook. The hook is flexibly linked to Mediator by a conserved hinge 19 and contacts the transcription initiation factor IIH (TFIIH) kinase that phosphorylates the carboxy (C)-terminal domain (CTD) of Pol II and was recently positioned on the PIC 20 . The hook also contains residues that crosslink to the CTD and reside in a previously described cradle 5 . These results provide a framework for understanding Mediator function, including its role in