T7 RNA polymerase – initially transcribing
The crystal structure of an initially transcribing T7 RNA polymerase with a 7 base transcript synthesized (3E2E). Note the nontemplate strand and template strand, with the RNA in a 7 base RNA-DNA hybrid. Comparing to the initiation structure, we see that the N-terminal domain remains bound to the duplex promoter DNA, but the entire assembly has rotated by about xx degrees and translated xx angstroms, including the protein beta hairpin, still lying in the central major groove. The melted bubble remains open, still stabilized by the hydrophobic “intercalating” loop that stacks onto the exposed base pair at position -5. Farther upstream, the Arg-rich loop still interacts with the far upstream AT-rich minor groove.
Note that in this structure, a downstream duplex is resolved.
Next: Elongating RNA polymerase, with an 8 base RNA-DNA hybrid.