Fig. 2: RNA exit tunnel is able to accommodate a double-stranded RNA helix.

a, Close-up view of the RNA exit tunnel. Cryo-EM density from Map B1 for the RNA (red) and the surrounding (gray) is shown. The tWH domain of RPA49 in the left panel and a section of subunit RPA2 obscuring the RNA exit tunnel in the right panel are hidden. b, Schematic representation of the nucleic acid scaffold. A second RNA primer (right) base pairs to the primer annealed to the DNA scaffold, forming a double-stranded helix owing to the sequence complementarity. The empty circles correspond to the RNA bases not visible in the cryo-EM density. c,d, Cross-sections through the RNA exit tunnel as indicated in a. Cryo-EM density corresponding to the protein components forming the tunnel is shown in gray. Residues within 5 Å of the RNA are shown represented as sticks. Residues making contacts with the RNA are annotated. Conservation between yeast and human Pol I residues is indicated as in the legend on the left of c. e, Cryo-EM density corresponding to the DNA–RNA hybrid is shown in gray. The bridge helix is in cartoon representation, and active site Asp residues are represented as sticks. f, Electrostatic charge distribution on the surface of (left to right) human Pol I EC, yeast Pol I (PDB: 5M64 (ref. ²⁵)), bovine Pol II (PDB: 5FLM³⁸), and human Pol III (PDB: 7AE1 (ref. ³³)). RNA in the exit tunnel is shown as a cartoon (red). In the left panel, outlines of the RPA43 subunit (blue) and tWH of the RPA49 (purple) are shown. The tunnel width was measured using ChimeraX from backbone to backbone using human Pol I residues RPA1-S508 to RPA49-K362, bovine Pol II residues RPB1-K434 to RPB2-Q838, human Pol III residues RPC1-Y434 to RPC2-A798, and yeast Pol I residues A190-G548 to A49-N354.