The complete enzyme or holoenzyme in E. coli has a molecular weight of ,460 kD. The holoenzyme (a2bbws) can be separated into two components: the core enzyme (a2bbw) and the sigma factor (the s polypeptide), which is concerned specifically with promoter recognition.

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#Unit 3. Fundamental Processes

U1 snRNA consist of four hairpins, one intron pairing strands and one sm binding domains.

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#Unit 3. Fundamental Processes

Once DNA has been melted, the trajectory of the individual strands within the enzyme is no longer constrained by the rigidity of the double helix, allowing DNA to make its 90° turn at the active site.

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#Unit 3. Fundamental Processes

There are RNA polymerase crystal structures that provide considerable insight into how the enzyme retains contact with its substrate while breaking and remaking bonds in the process of the nucleotide addition cycle and undergoing translocation by a Brownian ratchet mechanism.

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#Unit 3. Fundamental Processes

Unlike the other elements within the promoter, the UP-element is not recognized by s but is recognized by a carboxy-terminal domain of the subunit, called the aCTD .

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#Unit 3. Fundamental Processes

The aCTD is connected to the aNTD by a flexible linker. 

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#Unit 3. Fundamental Processes

Thus, although the aNTD is embedded in the body of the enzyme, the aCTD can reach the upstream element and can do so even when that element is not located immediately adjacent to the –35 region, but further upstream.