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Structure of the complete elongation complex of RNA polymerase II with basal factors

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Science  01 Sep 2017:
Vol. 357, Issue 6354, pp. 921-924
DOI: 10.1126/science.aan8552
  • Fig. 1 Crystal structure of Pol II EC with Spt5 KOW5 and Elf1.

    (A) The Spt4/5 and Elf1 constructs used in this study (numbers represent amino acid residue positions). The regions studied in the crystallographic and cryo-EM analyses are indicated by the red and green boxes, respectively. (B) Polyacrylamide gel electrophoresis analysis of in vitro transcription stimulation by Spt4/5 variants. (C) Overall structure of the Pol II EC–KOW5-Elf1 complex. (D) Close-up views of the Spt5 KOW5–binding site in two different orientations. (E) The Elf1-binding site and the DNA entry tunnel, shown in two different orientations. In the right panel, the N-terminal basic tail of Elf1 was presumed and is depicted as a dashed line. (F) The amino acid sequence of the Elf1 N-terminal tail, in which the basic residues are highlighted. β1 represents the first β strand of Elf1.

  • Fig. 2 Cryo-EM structure of Pol II EC with Spt4/5 and TFIIS.

    Overall structure of the complex showing (A) the “DNA-binding” face and (B) the “RNA-exit” face. (C) Interactions of Spt4 and Spt5 NGN-KOW1 with Pol II and DNA. The cryo-EM map (before sharpening) corresponding to Spt4, Spt5 NGN-KOW1, and the upstream DNA is overlaid. (D) Top view of the DNA exit tunnel. (E) Side view of the DNA exit tunnel. (F) The same view as in (E) with the surface electrostatic potentials of Spt4 and Spt5 NGN-KOW1. (G) Close-up view of the RNA exit site. The cryo-EM map (before sharpening) corresponding to the exiting RNA and Spt5 KOW4-KOW5 is overlaid. The KOW4-KOW5 linker and a possible path of the exiting RNA are depicted by a green line and a red dashed arrow, respectively. (H) Surface electrostatic potentials of the Spt5 KOW4-KOW5 domains, the Rpb1 dock, and the Rpb4/7 stalk.

  • Fig. 3 The architecture of the Pol II EC.

    (A) The DNA and RNA binding sites in the EC (the EFs are omitted). (B) The same as (A) but with bound Spt4/5, Elf1, and TFIIS (the composite model showing the DNA entry and exit tunnels). (C) The view of the RNA exit tunnel (the EFs are omitted). (D) The same as (C) but with the EFs (the expanded RNA exit tunnel). The KOW4-KOW5 linker, Pol II CTD, and Spt5 CTR are depicted by green, brown, and violet lines, respectively. (E) Schematic diagram summarizing the interactions between nucleic acids and EFs.

Supplementary Materials

  • Structure of the complete elongation complex of RNA polymerase II with basal factors

    Haruhiko Ehara, Takeshi Yokoyama, Hideki Shigematsu, Shigeyuki Yokoyama, Mikako Shirouzu, Shun-ichi Sekine

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods 
    • Figs. S1 to S16 
    • Tables S1 and S2 
    • Caption for Movie S1 
    • References 

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    Movie S1

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