Extended Data Fig. 2: The y-ins region and its interactions with downstream DNA in IC states.

a. Wall-eyed stereo view showing the starting y-ins AlphaFold model (UniProt ID: P13433, yellow) that was fitted to the density (turquoise model); the density for y-ins domain in the IC6 structure is contoured at 2.5σ. b. Relative positioning and interactions of y-ins domain with the downstream DNA in PmIC and all IC structures; yellow MTF1, light blue y-mtRNAP, cyan non-template, pink template DNA. The y-ins and MTF1 N-terminal domains define the downstream cleft, which interacts with the downstream DNA duplex. The interactions between the DNA and the downstream cleft are rearranged in IC structures. The DNA interacts only with MTF1 in PmIC, moves closer to y-ins in IC2, and interacts extensively with y-ins in IC5 to IC8, where the NT staircase structure is walled against MTF1. The structures are oriented as Fig. 1a (left panel).