The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (α2ββ'ω) and the promoter specificity σ subunit, has been determined at 4 angstrom resolution. Important structural features of the RNA polymerase and their roles in positioning σ within the initiation complex are delineated, as well as the role played by σ in modulating the opening of the RNA polymerase active-site channel. The two carboxyt-terminal domains of σ are separated by 45 angstroms on the surface of the RNA polymerase, but are linked by an extended loop. The loop winds near the RNA polymerase active site, where it may play a role in initiating nucleotide substrate binding, and out through the RNA exit channel. The advancing RNA transcript must displace the loop, leading to abortive initiation and ultimately to σ release.
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