Figure 6.

Conformational Changes during Isomerization and a Proposed “Coupled Load and Unwind” Initiation Model

(A) Conformational changes from RPc to RPo in σ⁵⁴ system. RNAP cleft opens initially from RPc to RPi to RPip before closes down in RPo. These are correlated with DNA path and σ⁵⁴ conformations. RNAP in surface representation, σ⁵⁴ and DNA in ribbon cartoon. Arrows indicate clamp opening.

(B) Proposed transcription initiation model. The initial closed complex is system specific; shown here is σ⁵⁴ RPc (PDB: 5NSR, labeled RPc1) where DNA is high above the RNAP cleft. RNAP is then converted to RPi in σ⁵⁴ system but could go to a conformation similar to those captured in yeast Pol II closed complex (RPc2, PDB: 5FZ5), before transition to RPc2 as captured in human Pol II closed complex (PDB: 5IYA) where the RNAP clamp is slightly open and DNA starts to bend into the RNAP cleft. In RPi1 (RPip), DNA makes a 30° kink in σ⁵⁴ (>60° in σ⁷⁰) and is at the entrance to the RNAP cleft with the clamp wide open. Clamp closure to RPo causes the DNA to load and unwind.

See also Figure S7.