Structural basis of transcription: RNA polymerase II at 2.8 angstrom ngstrom resolution

Structures of a 10-subunit yeast RNA polymerase II have been derived from t wo crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the stru ctures reveals a division of the polymerase into four mobile modules, inclu ding a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straig ht promoter DNA for the initiation of transcription. Three Loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during tra nscription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeabl e during RNA synthesis. The results also provide evidence for RNA exit in t he vicinity of the carboxyl-terminal repeat domain, coupling synthesis to R NA processing by enzymes bound to this domain.