Figure 3: Opening and closing of the DNA-binding clamp of RNAP.
From: The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration
(a) The structure of Tko RNAP is superimposed on the structures of Sso RNAP (left, blue, PDB: 3 HKZ) and yeast Pol II (right, green, PDB: 1 WCM) using the enzyme active sites as references. (b) Cryo-EM density map of Pfu RNAP (light grey mesh, EMD-1711) is overlaid with the Tko RNAP structure (main body of RNAP, grey; clamp, dark cyan; Rpo4/Rpo7 stalk, yellow-green; active site Mg, magenta sphere). The clamp of Pfu RNAP is indicated by a red arrow and in a closed-state. (c) Proposed motions of the clamp and stalk of archaeal RNAP. The open clamp (dark cyan) and stalk (yellow-green) observed in the Tko RNAP structure are superimposed on the closed clamp and stalk (grey) in the Sso RNAP structure. Motions and angles of the clamp and stalk from the closed to the open conformations are indicated. (d) Schematic representation of archaeal RNAP/Pol II showing the mobility of the DNA-binding cleft and the stalk.
