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Abstract

The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3  resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 39 end of the RNA in the nucleotide addition site. The 39 end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 59-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of ÒswitchesÓ at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. ProteinÐ nucleic acid contacts help explain DNA and RNA strand separation, the speci Þcity of RNA synthesis, Òabortive cyclingÓ during transcription initiation, and RNA and DNA translocation during transcription elongation.