Fig. 3: Conformational flexibility of M. tuberculosis RNAP.

Motions of the RNAP flap (a) and clamp (b). RNAP is shown as a molecular surface with the core subunits in gray and σ^B in yellow. The flap (β flap, β subunit aa 808–832) and clamp (β‘ subunit aa 1–413, 1219–1245; β subunit aa 1117–1140) domains are shown as cartoons with cylindrical helices. Rotation angles were measured in PyMol as described by²⁶. a The β flap position in Eσ^B (in red) relative to its position in RbpA/σ^A-RPo (blue, PDB ID 6C04) and in the T. thermophilus gp39/Eσ^A complex (pink, PDB ID 3WOD). b The clamp position in Eσ^B (in red) relative to RbpA/σ^A-RPo (blue, PDB ID 6C04) and RbpA/Eσ^A (orange, PDB ID 6C05). c Comparison of the σ^B and σ^A (PDB ID 6C05) structures. The σ subunits are shown as ribbons with domain σ1.1 in white, subregion R1.2 in red, NCR in yellow, R2 in goldenrod. d Motions of domain σ1.1. Superposition of σ1.1 in Eσ^B (dark red), RbpA/Eσ^A (light blue) and RbpA/CarD/Eσ^A (green, PDB ID 6EDT). The RNAP core is shown as a molecular surface in gray. σ^A and σ^B are shown as ribbons; dwDNA (blue): downstream fragment of promoter DNA duplex.