Fig. 1: Structure of RNAP elongation complex. | Nature Communications

Fig. 1: Structure of RNAP elongation complex.

From: Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD

Fig. 1

a Left-hand graph shows multi-round transcription assays of purified RNAP core supplemented with increasing amounts of HelD (as a ratio with RNAP), HelD only (0:32, negative control) and the native RNAP-HelD complex purified from B. subtilis (RNAP-HelD). Black dots represent data obtained using wild-type HelD, magenta dots, data obtained using HelD K239A. The right-hand graph shows ATPase assays of wild-type HelD, HelD K239A, and BSA (negative control). Error bars, SD. Each experiment was performed three times in technical duplicate. Source data are provided in the Source Data files. b, c Cryo-EM reconstruction of the RNAP elongation complex (EC). The electron density map is semi-transparent in the same colours as the subunits in the cartoon structure: αI beige, αII brown, β azure, β’ yellow, ω light green, template DNA purple, non-template DNA pink, and RNA orange. The dotted circles show the location of the βln5 insertion, ε binding site (b) and β E696-G705 insertion (c), respectively. The upstream and downstream sides of RNAP are indicated in c. d Top shows a schematic of the nucleic acids coloured as in panels b and c. +1 represents the template DNA nucleotide positioned within the active site. + integers represent nucleotides base paired as DNA on the downstream side of RNAP, and −ve integers represent the DNA-RNA hybrid on the upstream side. The arrow indicates the position of the unpaired +1 nucleotide in the active site of RNAP in the lower part of the panel. Intermolecular bonds (polar and non-polar) are indicated by the dashed lines. Relevant template (t) and non-template (nt) nucleotides are numbered appropriately and amino acids shown with the RNAP subunit as a prefix. The catalytic Mg2+ ion is shown as a green sphere to indicate the active site. e An enlarged view of the upstream side of the EC close to the entry of the RNA exit channel. The salt bridge formed between β R800 and β’ D245 is shown as black dashed line. The space below the β’ lid that could accommodate a 9th DNA-RNA base pair is shown as a dotted rectangle, with the β’ rudder helping guide RNA towards the β’ lid and the RNA exit channel.

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