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RNA polymerase II–TFIIB structure and mechanism of transcription initiation

Nature volume 462, pages 323–330 (2009)Cite this article

Abstract

To initiate gene transcription, RNA polymerase II (Pol II) requires the transcription factor IIB (B). Here we present the crystal structure of the complete Pol II–B complex at 4.3 Å resolution, and complementary functional data. The results indicate the mechanism of transcription initiation, including the transition to RNA elongation. Promoter DNA is positioned over the Pol II active centre cleft with the ‘B-core’ domain that binds the wall at the end of the cleft. DNA is then opened with the help of the ‘B-linker’ that binds the Pol II rudder and clamp coiled-coil at the edge of the cleft. The DNA template strand slips into the cleft and is scanned for the transcription start site with the help of the ‘B-reader’ that approaches the active site. Synthesis of the RNA chain and rewinding of upstream DNA displace the B-reader and B-linker, respectively, to trigger B release and elongation complex formation.

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Figure 1: Structure of Pol II–B complex.
Figure 2: Models of closed and open complexes.
Figure 3: B-linker and DNA opening.
Figure 4: B-reader and DNA start site scanning.
Figure 5: Initiation–elongation transition and PIC architecture.
Figure 6: Eukaryotic and bacterial transcription initiation complexes.

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Protein Data Bank

Data deposits

Atomic coordinates and structure factors of the complete Pol II–B complex crystal structure have been deposited with the Protein Data Bank under accession number 3K1F. The closed and open complex models can be downloaded from http://www.lmb.uni-muenchen.de/cramer.

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Acknowledgements

P.C. was supported by the Deutsche Forschungsgemeinschaft, the Sonderforschungsbereich SFB646, the Transregio 5, the Forschergruppe ‘Regulation und Mechanismen der Ribosomen-Biogenese’, the Nanosystems Initiative Munich (NIM), the Ernst-Jung-Stiftung, and the Fonds der chemischen Industrie. M.S. was supported by the Boehringer-Ingelheim-Fonds and Elitenetzwerk Bayern. Part of this work was performed at the ESRF at Grenoble, France, and at the Swiss Light Source (SLS) at the Paul Scherrer Institut, Villigen, Switzerland. M.T. and M.E.Z. were supported by the DFG Forschergruppe ‘Regulation und Mechanismen der Ribosomenbiogenese’. We thank members of the Cramer laboratory, in particular E. Lehmann and K. Maier, and members of the Thomm laboratory, in particular P. Decartes, W. Forster and F. Hirchaud. We thank K. Römer and the Römer-Stiftung for support.

Author Contributions D.K. carried out structure determination and modelling. M.E.Z. carried out archaeal biochemical assays. K.-J.A. prepared and measured the crystals and did the initial data processing. M.E.Z. and M.S. carried out yeast analysis. K.L. provided technical assistance. M.T. supervised the archaeal biochemical work. P.C. designed and supervised the project and prepared the manuscript.

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  1. Karim-Jean Armache

    Present address: Present address: Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA.,

  2. Dirk Kostrewa, Mirijam E. Zeller and Karim-Jean Armache: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany,

    Dirk Kostrewa, Karim-Jean Armache, Martin Seizl, Kristin Leike & Patrick Cramer

  2. Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany

    Mirijam E. Zeller & Michael Thomm

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Correspondence to Patrick Cramer.

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Kostrewa, D., Zeller, M., Armache, KJ. et al. RNA polymerase II–TFIIB structure and mechanism of transcription initiation. Nature 462, 323–330 (2009). https://doi.org/10.1038/nature08548

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