Article

Structures of transcription pre-initiation complex with TFIIH and Mediator

  • Nature volume 551, pages 204209 (09 November 2017)
  • doi:10.1038/nature24282
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Abstract

For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC–core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the ‘E-bridge’ helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC–core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.

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Acknowledgements

We thank S. Neyer, C. Bernecky, C. Burzinski, S. Vos, L. Farnung and other members of the Cramer laboratory for help. We thank C.-T. Lee and I. Parfentev from the Urlaub group for mass spectrometry. H.U. was supported by the Deutsche Forschungsgemeinschaft (SFB860). P.C. was supported by the Deutsche Forschungsgemeinschaft (SFB860, SPP1935), the Advanced Grant TRANSREGULON (grant agreement no. 693023) of the European Research Council, and the Volkswagen Foundation.

Author information

Affiliations

  1. Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany

    • S. Schilbach
    • , M. Hantsche
    • , D. Tegunov
    • , C. Dienemann
    • , C. Wigge
    • , H. Urlaub
    •  & P. Cramer
  2. University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany

    • H. Urlaub

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Contributions

S.S. carried out all experiments and data analysis except for the following. M.H. carried out EDC crosslinking and Mediator modelling. C.D. performed TFIIE modelling and established a protocol for cPIC formation. D.T. wrote and applied the WarpCraft software. C.W. supervised EM data collection. H.U. conducted mass spectrometry. P.C. designed and supervised research. S.S. and P.C. prepared the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to P. Cramer.

Reviewer Information Nature thanks S. Hahn, X. Zhang and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Tables 1-4.

  2. 2.

    Life Sciences Reporting Summary

Zip files

  1. 1.

    Supplementary Data

    WarpCraft source code. This zipped file contains the C# code used to perform the flexible refinement and a precompiled binary.

Videos

  1. 1.

    Overview of the WarpCraft cryo-EM map and ribbon model of the PIC structure

    Video showing an overview of the WarpCraft cryo-EM map and ribbon model of the PIC structure.

  2. 2.

    Overview of the WarpCraft cryo-EM map and ribbon model of the PIC-cMed structure

    Video showing an overview of the WarpCraft cryo-EM map and ribbon model of the PIC-cMed structure.

  3. 3.

    Conformational changes in the cMed middle module

    Conformational changes in the cMed middle module between the crystal structure of free cMed5 and the observed PIC-bound state.

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