Fig. 5: Structures of Pol I paused by an Ap site at i + 1 in the presence of AMPCPP. | Nature Communications

Fig. 5: Structures of Pol I paused by an Ap site at i + 1 in the presence of AMPCPP.

From: Cryo-EM uncovers a sequential mechanism for RNA polymerase I pausing and stalling at abasic DNA lesions

Fig. 5

a Overall Ap-NAC structure and close-up view around AMPCPP in the A-site. H-bonds are shown as green dotted lines. b Comparison between Ap-NAC and the same structure where GMPCPP has been modelled. H-bonds and hydrophobic contacts are shown as green and orange dotted lines, while an orange star denotes a clash. c Superposition of Ap-NAC (colors) with Closed Ap-PEC (grey). d Superposition between Ap-NAC (colors) and Pol I with undamaged DNA in a pre-insertion state in the presence of GMPCPP in the A-site (PDB code 6HKO, grey). e Overall Ap-NEC structure and close-up view around AMPCPP in the E-site. The close-up view is rotated ~120° along the bridge helix with respect to that in (a). f Superposition of Ap-NEC (colors) with Ap-NAC (grey). g Superposition of Ap-NEC (colors) with Pol II with ATP in the E-site (PDB code 1R9T, grey). View is as in (e).

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