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Structure of the Mediator head module

Abstract

Gene transcription by RNA polymerase (Pol) II requires the coactivator complex Mediator. Mediator connects transcriptional regulators and Pol II, and is linked to human disease1,2,3,4. Mediator from the yeast Saccharomyces cerevisiae has a molecular mass of 1.4 megadaltons and comprises 25 subunits that form the head, middle, tail and kinase modules5,6,7. The head module constitutes one-half of the essential Mediator core8, and comprises the conserved9 subunits Med6, Med8, Med11, Med17, Med18, Med20 and Med22. Recent X-ray analysis of the S. cerevisiae head module at 4.3 Å resolution led to a partial architectural model with three submodules called neck, fixed jaw and moveable jaw10. Here we determine de novo the crystal structure of the head module from the fission yeast Schizosaccharomyces pombe at 3.4 Å resolution. Structure solution was enabled by new structures of Med6 and the fixed jaw, and previous structures of the moveable jaw11 and part of the neck12, and required deletion of Med20. The S. pombe head module resembles the head of a crocodile with eight distinct elements, of which at least four are mobile. The fixed jaw comprises tooth and nose domains, whereas the neck submodule contains a helical spine and one limb, with shoulder, arm and finger elements. The arm and the essential shoulder contact other parts of Mediator. The jaws and a central joint are implicated in interactions with Pol II and its carboxy-terminal domain, and the joint is required for transcription in vitro. The S. pombe head module structure leads to a revised model of the S. cerevisiae module, reveals a high conservation and flexibility, explains known mutations, and provides the basis for unravelling a central mechanism of gene regulation.

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Figure 1: Structures of Med6 and Med17C–Med11C–Med22C.
Figure 2: Structure of Sp Mediator head module.
Figure 3: Structural elements and surface conservation.
Figure 4: Head module integrity and interactions.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinate files and structure factorswere deposited in the Protein Data Bank under accession codes 4H61 (Sp Med6), 4H62 (Sc Med17C–Med11C–Med22C) and 4H63 (Sp head module). See Supplementary Data for the coordinate file for the revised Sc head module model.

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Acknowledgements

We thank S. Baumli, A. C. Cheung, A. Imhof and C. Schmidt for help. We acknowledge the crystallization facility at the Max Planck Institute of Biochemistry, Martinsried. Diffraction data were collected at the Swiss Light Source, Villigen, Switzerland. M.S. was supported by a Boehringer Ingelheim fellowship and the Elite Network of Bavaria. P.C. was supported by the Deutsche Forschungsgemeinschaft, SFB646, TR5, GraKo1721, SFB960, CIPSM, NIM, an Advanced Grant of the European Research Council, the LMUinnovativ project Bioimaging Network, the Vallee Foundation, and the Jung-Stiftung.

Author information

Authors and Affiliations

Authors

Contributions

L.L. designed crystallization constructs, established expression and purification strategies for head modules, solved the Med6 and Med17C–Med11C–Med22C structures, carried out crystallographic data analysis for Sp head module structure determination, built the Sc head module model, generated yeast strains, and performed in vivo studies. C.P. optimized Sp head module purification, purified and crystallized the Sp head module variants, and prepared heavy metal derivatives. L.L. and C.P. collected diffraction data for the head module and carried out model building and structural analysis. M.S. contributed to establishing expression and purification strategies and carried out transcription assays. L.W. provided technical help. F.K. optimized transcription assays. P.C. initiated and supervised the project. P.C., L.L., C.P. and M.S. prepared the manuscript.

Corresponding authors

Correspondence to Laurent Larivière or Patrick Cramer.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Notes 1-2, Supplementary Figures 1-12, Supplementary Tables 1-3 and Supplementary References. (PDF 10571 kb)

Supplementary Data

This file contains the coordinates in PDB format for the revised Sc Mediator head module model. Subunits Med6, Med8, Med11, Med17, Med18, Med20 and Med22 correspond to chains F, H, K, Q, R, T and V, respectively. This file was originally missing and was added online on 19 December 2012. (TXT 457 kb)

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Larivière, L., Plaschka, C., Seizl, M. et al. Structure of the Mediator head module. Nature 492, 448–451 (2012). https://doi.org/10.1038/nature11670

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