Structure of wild-type yeast RNA polymerase II and location of Rpb4 and Rpb7

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Abstract
The three‐dimensional structure of wild‐type yeast RNA polymerase II has been determined at a nominal resolution of 24 Å. A difference map between this structure and that of the polymerase lacking subunits Rpb4 and Rpb7 showed these two subunits forming part of the floor of the DNA‐binding (active center) cleft, and revealed a slight inward movement of the protein domain surrounding the cleft. Surface plasmon resonance measurements showed that Rpb4 and Rpb7 stabilize a minimal pre‐initiation complex containing promoter DNA, TATA box‐binding protein (TBP), transcription factor TFIIB and the polymerase. These findings suggest that Rpb4 and Rpb7 play a role in coupling the entry of DNA into the active center cleft to closure of the cleft. Such a role can explain why these subunits are necessary for promoter‐specific transcription in vitro and for a normal stress response in vivo.