Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies by Yun Yang, Vidya C. Darbari, Nan Zhang, Duo Lu, Robert Glyde, Yi-Ping.

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Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies by Yun Yang, Vidya C. Darbari, Nan Zhang, Duo Lu, Robert Glyde, Yi-Ping Wang, Jared T. Winkelman, Richard L. Gourse, Katsuhiko S. Murakami, Martin Buck, and Xiaodong Zhang Science Volume 349(6250):882-885 August 21, 2015 Published by AAAS

Fig. 1 Structure of complete RNAP-σ54. Structure of complete RNAP-σ54. (A) Structure and schematic diagram of σ54. (B) Structure of σ70 (PDB 4YG2) with similar functional domains colored accordingly. (C) Holoenzyme in different orientations, RNAP core in cylinders. β, cyan; β′, salmon pink; α, gray; ω, pale blue; σ54 in ribbon and colored as in (A); DS, downstream; US, upstream. (D) Residues of β and β′ subunits that are cross-linked to σ54 are mapped onto the structure and colored in yellow. (E) Electron density map and structural model of RNAP-σ54–DNA. Yun Yang et al. Science 2015;349:882-885 Published by AAAS

Fig. 2 Functional domains of σ54 and interactions with RNAP core. Functional domains of σ54 and interactions with RNAP core. (A) Detailed view of the CBD and RNAP interactions. (B) RI and RIII. (C) DNA-RNA channels, with DNA, orange, and RNA, magenta. (D) Overlay with RII.1, RII.2, and RII.3. Yun Yang et al. Science 2015;349:882-885 Published by AAAS

Fig. 3 Comparisons of σ54 and σ70 holoenzymes. Comparisons of σ54 and σ70 holoenzymes. (A) RNAP-σ54 with RNAP displayed as spheres and σ54 as surface. (B) RNAP-σ70, same view as in (A). (C) Elongation complex (PDB code 2O5J). Yun Yang et al. Science 2015;349:882-885 Published by AAAS

Fig. 4 Regulatory elements of σ54 and comparison with σ70, TFIIB, and Pol I. Regulatory elements of σ54 and comparison with σ70, TFIIB, and Pol I. (A) σ54, (B) σ70, and (C) TFIIB in relation to template strand (gold), as defined in the complex with a full transcription bubble (4YLN). (D to F) Comparison of σ54 with σ70, Pol I (4C2M), and TFIIB (4BBS) in the RNAP DNA-RNA channel; structures are superposed on the bridge helix. σ54 represented as spheres; σ70, TFIIB, and Pol I expander are shown as ribbons; and RNAP as cylinders. Yun Yang et al. Science 2015;349:882-885 Published by AAAS