Extended Data Fig. 4: Cryo-EM analysis of Pol II-minimal Alu-RA.
From: Mechanism of mammalian transcriptional repression by noncoding RNA
a, Cryo-EM micrograph representative field of view, -1.7 μm defocus. One of a total of 7,588 micrographs is shown. b, Representative 2D classes. c, Processing tree outlining the steps taken to generate the Pol II-minimal Alu-RA reconstructions. d, Angular distribution plot for the Pol II-minimal Alu-RA reconstructions. e, Fourier shell correlation plot for the Pol II-minimal Alu-RA reconstructions, the Pol II-minimal Alu-RA phase-randomized masked maps, and the model-versus-map correlation for the Pol II-minimal Alu-RA alternative conformation reconstruction and the model. f, Locally-filtered Pol II-minimal Alu-RA reconstructions colored by estimated local resolution. The Pol II-minimal Alu-RA canonical conformation reconstruction was not B-factor sharpened. g, Top-front and side views of 8-Å-filtered Pol II-minimal Alu-RA canonical and alternative conformation densities compared to the path of nucleic acids in a transcription elongation complex (PDB ID 5OIK)27. Minimal Alu-RA density is shown in semi-transparent gray. Compare to Fig. 1b,c. h, Schematics showing the secondary structures of the canonical and alternative conformations of minimal Alu-RA. Guanosine, green; cytidine, cyan; adenosine, blue; uridine, orange. i, Putative assignment of the regions of Alu-RA that bind in the DNA-RNA hybrid (putative lower stem) and the downstream DNA-binding (putative upper stem) regions of the Pol II cleft. Alu-RA difference density (purple), upper and lower stems (gray bars).
