E. coli Transcript Cleavage Factor GreA

Transcription elongation factors stimulate the activity of the RNA polymerase by increasing the overall elongation rate and the completion of RNA chains. E. coli GreA is one such factor. It acts by inducing cleavage of the transcript within the RNA polymerase, followed by release of the RNA 3'-terminal fragment. The crystal structure of GreA has been determined at 2.2 Å resolution. The structure contains an amino-terminal domain consisting of antiparallel -helical coiled-coil dimer (see strereodiargam on right) which extends into solution.
The 3D structure of GreA (whose water accessible surface is shown in solid white in picture on left) exhibits an unusually asymmetric charge distribution indicating how GreA may interact with the elongation complex and transcript. Positive and negative isopotential contours are shown in red and blue respectively. GreA fragment contacting transcript shown in green. Another representation of charge distribution and water-accessible surface showing three different views of GreA is also available.
To learn more about GreA function and structure check out GreA Protein page by Erec Stebbins.

E. coli RNA Polymerase Core Enzyme
E. coli RNAP contains a catalytic core of two subunits, one ß, and one ß' subunit, with molecular masses of 36.5, 151, and 155 kDa respectively, which is fully active in RNA polymerization. Binding of one of a variety of regulatory subunits (normally , with molecular mass 70.2 kDa), to form the holoenzyme, is required for specific initiation from promoters.

These are the different views of the core RNA polymerase molecules as they observed on the surface of a lipid bilayer tube. Each picture shows three molecules which appear linked. It happens because negative stain does not penetrate between the molecules due to their tight packing within a helical crystal. Our interpretation of a single molecule (see picture on the left) is based on comparisons with previously determined structures of E. coli holoenzyme and yeast RNA polymerase II. The overall dimensions of a single core molecule in the crystal are 85 x 105 x 140 Å. The most striking feature of the core structure is a thumb-like projection surrounding a channel. The channel is 25 Å in diameter and can easily accommodate double stranded DNA. For more information on this structure see our recent paper (Polyakov et al., Cell 1995, 83, pp 365-373).

E. coli RNA Polymerase Holoenzyme

The three-dimensional structure RNA polymerase holoenzyme was determined by electron microscopy of negatively stained, two-dimensional crystals tilted at various angles to the incident electron beam in Roger Kornberg lab (Stanford University) by Darst et al. in 1989 (Nature 340, pp. 730-732) at ~ 28 Å resolution. The thumb in holoenzyme structure unlike in core RNA polymerase defines a deep open groove on the surface of the molecule. The irregularly shaped holoenzyme molecule is approximately 100 x 100 x 160 Å in size.

Yeast RNA Polymerase II

The structure of Yeast RNA Polymerase II (pol II) was determined by 3D reconstitution from electron micrographs of 2D crystals at ~16 Å in Roger Kornberg lab (Stanford University) by Darst et al. in 1991 (Cell 66, pp 121-128). The picture shows two different views of pol II molecules down the DNA channel axis. The most prominent feature of the structure is an arm of protein density surrounding a channel about 25 Å in diameter, similar to that found previously for E. coli RNA polymerase. The 25 Å-diameter channel bifurcates on one face of the protein, connecting with a 25 Å-wide groove and with a channel about half as wide. The 25 Å channel and groove, and the narrow channel, may bind double- and single-stranded nucleic acids, respectively. The overall dimensions of of a single pol II molecule in 3D are about 140 x 136 x 110 Å. Yeast pol II used for crystallization lacked two subunits (4 and 7) which are dispensable for RNA chain elongation

You may want to look at side by side comparison of Yeast RNA Polymerase II, E. coli core RNA polymerase and holoenzyme. The opposite view of the same picture is also available.