Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Structure of the human Mediator–RNA polymerase II pre-initiation complex


Mediator is a conserved coactivator complex that enables the regulated initiation of transcription at eukaryotic genes1,2,3. Mediator is recruited by transcriptional activators and binds the pre-initiation complex (PIC) to stimulate the phosphorylation of RNA polymerase II (Pol II) and promoter escape1,2,3,4,5,6. Here we prepare a recombinant version of human Mediator, reconstitute a 50-subunit Mediator–PIC complex and determine the structure of the complex by cryo-electron microscopy. The head module of Mediator contacts the stalk of Pol II and the general transcription factors TFIIB and TFIIE, resembling the Mediator–PIC interactions observed in the corresponding complex in yeast7,8,9. The metazoan subunits MED27–MED30 associate with exposed regions in MED14 and MED17 to form the proximal part of the Mediator tail module that binds activators. Mediator positions the flexibly linked cyclin-dependent kinase (CDK)-activating kinase of the general transcription factor TFIIH near the linker to the C-terminal repeat domain of Pol II. The Mediator shoulder domain holds the CDK-activating kinase subunit CDK7, whereas the hook domain contacts a CDK7 element that flanks the kinase active site. The shoulder and hook domains reside in the Mediator head and middle modules, respectively, which can move relative to each other and may induce an active conformation of the CDK7 kinase to allosterically stimulate phosphorylation of the C-terminal domain.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Structure of the human Mediator–PIC complex.
Fig. 2: Features of the structure of human Mediator.
Fig. 3: Interactions between Mediator and the core PIC.
Fig. 4: Interactions between Mediator and TFIIH kinase.

Data availability

The cryo-EM density reconstructions and models were deposited with the Electron Microscopy Data Bank (EMDB) (accession codes EMD-12609 for Mediator in complex with the Pol II stalk and EMD-12610 for Mediator in complex with the PIC) and with the Protein Data Bank (PDB) (accession code 7NVR). All data are available in the Article or its supplementary files. Source data are provided with this paper.


  1. 1.

    Malik, S. & Roeder, R. G. Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. Trends Biochem. Sci. 25, 277–283 (2000).

    CAS  PubMed  Google Scholar 

  2. 2.

    Kornberg, R. D. Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30, 235–239 (2005).

    CAS  PubMed  Google Scholar 

  3. 3.

    Schier, A. C. & Taatjes, D. J. Structure and mechanism of the RNA polymerase II transcription machinery. Genes Dev. 34, 465–488 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Kim, Y. J., Björklund, S., Li, Y., Sayre, M. H. & Kornberg, R. D. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77, 599–608 (1994).

    CAS  PubMed  Google Scholar 

  5. 5.

    Malik, S. & Roeder, R. G. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat. Rev. Genet. 11, 761–772 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Conaway, R. C. & Conaway, J. W. Origins and activity of the Mediator complex. Semin. Cell Dev. Biol. 22, 729–734 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Plaschka, C. et al. Architecture of the RNA polymerase II–Mediator core initiation complex. Nature 518, 376–380 (2015).

    CAS  PubMed  ADS  Google Scholar 

  8. 8.

    Robinson, P. J. et al. Structure of a complete Mediator–RNA polymerase II pre-initiation complex. Cell 166, 1411–1422 (2016).

    CAS  Article  Google Scholar 

  9. 9.

    Schilbach, S. et al. Structures of transcription pre-initiation complex with TFIIH and Mediator. Nature 551, 204–209 (2017).

    CAS  Article  ADS  Google Scholar 

  10. 10.

    Elmlund, H. et al. The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II. Proc. Natl Acad. Sci. USA 103, 15788–15793 (2006).

    CAS  PubMed  ADS  Google Scholar 

  11. 11.

    Tsai, K. L. et al. A conserved Mediator–CDK8 kinase module association regulates Mediator–RNA polymerase II interaction. Nat. Struct. Mol. Biol. 20, 611–619 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Knuesel, M. T., Meyer, K. D., Bernecky, C. & Taatjes, D. J. The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function. Genes Dev. 23, 439–451 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Chadick, J. Z. & Asturias, F. J. Structure of eukaryotic Mediator complexes. Trends Biochem. Sci. 30, 264–271 (2005).

    CAS  PubMed  Google Scholar 

  14. 14.

    Larivière, L., Seizl, M. & Cramer, P. A structural perspective on Mediator function. Curr. Opin. Cell Biol. 24, 305–313 (2012).

    PubMed  Google Scholar 

  15. 15.

    Plaschka, C., Nozawa, K. & Cramer, P. Mediator architecture and RNA polymerase II interaction. J. Mol. Biol. 428, 2569–2574 (2016).

    CAS  PubMed  Google Scholar 

  16. 16.

    Imasaki, T. et al. Architecture of the Mediator head module. Nature 475, 240–243 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Larivière, L. et al. Structure of the Mediator head module. Nature 492, 448–451 (2012).

    PubMed  ADS  Google Scholar 

  18. 18.

    Robinson, P. J., Bushnell, D. A., Trnka, M. J., Burlingame, A. L. & Kornberg, R. D. Structure of the Mediator Head module bound to the carboxy-terminal domain of RNA polymerase II. Proc. Natl Acad. Sci. USA 109, 17931–17935 (2012).

    CAS  PubMed  ADS  Google Scholar 

  19. 19.

    Wang, X. et al. Redefining the modular organization of the core Mediator complex. Cell Res. 24, 796–808 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Tsai, K. L. et al. Subunit architecture and functional modular rearrangements of the transcriptional mediator complex. Cell 157, 1430–1444 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Tsai, K. L. et al. Mediator structure and rearrangements required for holoenzyme formation. Nature 544, 196–201 (2017).

    CAS  PubMed  PubMed Central  ADS  Google Scholar 

  22. 22.

    Cevher, M. A. et al. Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat. Struct. Mol. Biol. 21, 1028–1034 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Nozawa, K., Schneider, T. R. & Cramer, P. Core Mediator structure at 3.4 Å extends model of transcription initiation complex. Nature 545, 248–251 (2017).

    CAS  PubMed  ADS  Google Scholar 

  24. 24.

    Egly, J. M. & Coin, F. A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor. DNA Repair 10, 714–721 (2011).

    CAS  PubMed  Google Scholar 

  25. 25.

    Aibara, S., Schilbach, S. & Cramer, P. Structures of mammalian RNA polymerase II pre-initiation complexes. Nature (2021).

  26. 26.

    Kokic, G. et al. Structural basis of TFIIH activation for nucleotide excision repair. Nat. Commun. 10, 2885 (2019).

    PubMed  PubMed Central  ADS  Google Scholar 

  27. 27.

    Vos, S. M., Farnung, L., Urlaub, H. & Cramer, P. Structure of paused transcription complex Pol II–DSIF–NELF. Nature 560, 601–606 (2018).

    CAS  PubMed  PubMed Central  ADS  Google Scholar 

  28. 28.

    Greber, B. J. et al. The cryoelectron microscopy structure of the human CDK-activating kinase. Proc. Natl Acad. Sci. USA 117, 22849–22857 (2020).

    CAS  PubMed  Google Scholar 

  29. 29.

    Asturias, F. J., Jiang, Y. W., Myers, L. C., Gustafsson, C. M. & Kornberg, R. D. Conserved structures of Mediator and RNA polymerase II holoenzyme. Science 283, 985–987 (1999).

    CAS  PubMed  ADS  Google Scholar 

  30. 30.

    Bourbon, H. M. et al. A unified nomenclature for protein subunits of Mediator complexes linking transcriptional regulators to RNA polymerase II. Mol. Cell 14, 553–557 (2004).

    CAS  PubMed  Google Scholar 

  31. 31.

    El Khattabi, L. et al. A pliable Mediator acts as a functional rather than an architectural bridge between promoters and enhancers. Cell 178, 1145–1158 (2019).

    CAS  PubMed  Google Scholar 

  32. 32.

    Zhao, H. et al. Structure of mammalian Mediator complex reveals Tail module architecture and interaction with a conserved core. Nat. Commun. 12, 1355 (2021).

    CAS  PubMed  PubMed Central  ADS  Google Scholar 

  33. 33.

    Lolli, G., Lowe, E. D., Brown, N. R. & Johnson, L. N. The crystal structure of human CDK7 and its protein recognition properties. Structure 12, 2067–2079 (2004).

    CAS  PubMed  Google Scholar 

  34. 34.

    Wood, D. J. & Endicott, J. A. Structural insights into the functional diversity of the CDK–cyclin family. Open Biol. 8, 180112 (2018).

    PubMed  PubMed Central  Google Scholar 

  35. 35.

    Peissert, S., Schlosser, A., Kendel, R., Kuper, J. & Kisker, C. Structural basis for CDK7 activation by MAT1 and cyclin H. Proc. Natl Acad. Sci. USA 117, 26739–26748 (2020).

    CAS  PubMed  Google Scholar 

  36. 36.

    Abdella, R. et al. Structure of the human Mediator-bound transcription preinitiation complex. Science 372, 52–56 (2021).

    CAS  PubMed  PubMed Central  ADS  Google Scholar 

  37. 37.

    Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8 Å resolution. Science 292, 1863–1876 (2001).

    CAS  PubMed  ADS  Google Scholar 

  38. 38.

    Gradia, S. D. et al. MacroBac: new technologies for robust and efficient large-scale production of recombinant multiprotein complexes. Methods Enzymol. 592, 1–26 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Weissmann, F. et al. biGBac enables rapid gene assembly for the expression of large multisubunit protein complexes. Proc. Natl Acad. Sci. USA 113, E2564–E2569 (2016).

    CAS  PubMed  Google Scholar 

  40. 40.

    Farnung, L., Vos, S. M., Wigge, C. & Cramer, P. Nucleosome–Chd1 structure and implications for chromatin remodelling. Nature 550, 539–542 (2017).

    CAS  PubMed  PubMed Central  ADS  Google Scholar 

  41. 41.

    Kastner, B. et al. GraFix: sample preparation for single-particle electron cryomicroscopy. Nat. Methods 5, 53–55 (2008).

    CAS  PubMed  Google Scholar 

  42. 42.

    Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).

    PubMed  PubMed Central  Google Scholar 

  43. 43.

    Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45.

    Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

    PubMed  PubMed Central  Google Scholar 

  46. 46.

    Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Casañal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of electron cryo-microscopy and crystallographic data. Protein Sci. 29, 1055–1064 (2020).

    Google Scholar 

  49. 49.

    Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).

    CAS  Google Scholar 

  50. 50.

    Prisant, M. G., Williams, C. J., Chen, V. B., Richardson, J. S. & Richardson, D. C. New tools in MolProbity validation: CaBLAM for cryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics. Protein Sci. 29, 315–329 (2020).

    CAS  PubMed  Google Scholar 

  51. 51.

    Kidmose, R. T. et al. Namdinator—automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps. IUCrJ 6, 526–531 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Notredame, C., Higgins, D. G. & Heringa, J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000).

    CAS  PubMed  Google Scholar 

  53. 53.

    Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320–W324 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references


We thank past and present members of the P.C. laboratory, particularly U. Neef, P. Rus and F. Grabbe for maintenance of the insect cell culture and purification of the recombinant human initiation factors; and we thank C. Dienemann and U. Steuerwald for maintenance of the cryo-EM facility. S.R. was supported by a Peter-and-Traudl-Engelhorn postdoctoral fellowship; S.A. was supported by an H2020 Marie Curie Individual Fellowship (894862); and P.C. was supported by the Deutsche Forschungsgemeinschaft (EXC 2067/1 39072994, SFB860 and SPP2191) and the ERC Advanced Investigator Grant CHROMATRANS (grant agreement no. 882357).

Author information




S.R. performed all experiments and data analysis, except for the following: S.S. established the human PIC preparation; S.A. provided human PIC coordinates; S.A. and S.S. assisted with data processing and structural modelling; and C.D. assisted with cryo-EM grid preparation and data collection. P.C. designed and supervised research. S.R., S.S., S.A. and P.C. interpreted the data and wrote the manuscript.

Corresponding author

Correspondence to Patrick Cramer.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks Steve Hahn and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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

Extended data figures and tables

Extended Data Fig. 1 Preparation of the human Mediator–PIC complex.

a, Size-exclusion chromatography of recombinant human Mediator shows a single peak. SDS–PAGE analysis (replicated three times) shows the presence of 20 Mediator subunits, confirmed by mass spectrometry (not shown). Raw SDS–PAGE data are provided in Supplementary Fig. 2. b, SDS–PAGE analysis of the human Mediator–PIC complex after isolation from a sucrose gradient (replicated three times). Raw SDS–PAGE data are provided in Supplementary Fig. 2. c, Recombinant 20-subunit human Mediator is able to stimulate Pol II CTD phosphorylation by CDK7 in the presence of ATP. Pol II CTD phosphorylation was assessed by western blotting against phosphorylated Ser5 of the CTD heptad repeat. An antibody against RPB3 was used to obtain the loading control. Experiments were performed in triplicate (P1–P3 and M1–M3) and a negative control sample without ATP (PC and MC) was included to exclude prior CTD phosphorylation. The bar diagram illustrates an around 4.5-fold stimulation of Pol II CTD phosphorylation in the Mediator–PIC samples over the PIC samples. Data are mean ± s.d. of three independent experiments (replicated three times). The mean value of the triplicates was used as the centre measure for error bars (mean = 4.47). Statistical significance with a P value of 3.43 × 10−6 was determined using a one-tailed unpaired t-test (***P < 0.001, **P < 0.01, *P < 0.05). Raw data for the western blots are available in Supplementary Fig. 2.

Source data

Extended Data Fig. 2 Cryo-EM data processing.

a, Representative cryo-EM micrograph of the human Mediator–PIC complex (replicated more than 20,000 times). Scale bar, 300 Å. b, Processing tree describing particle classification. Reconstructions that gave rise to maps used for model building are indicated (blue for focused maps, green for overall maps). Regions corresponding to the core PIC (cPIC), TFIIH (including the CAK), DNA, and Mediator are coloured in grey, pink, dark blue and cyan, and blue, respectively. c, Reconstructions coloured by their local resolution as estimated using RELION. In the angular distribution plots, colour indicates particle representation (white areas indicate unpopulated angles).

Extended Data Fig. 3 FSCs of reconstructions and cryo-EM density.

a, Solvent-corrected ‘gold-standard’ FSCs for the reconstructions shown in Extended Data Fig. 2c. Unmasked (green), masked (blue), and phase-randomized (red) FSCs are also shown. b, Schematic representation of Mediator subunit domain architecture. Regions contributing to submodules are coloured according to the S. pombe cMed structure23. Unassigned regions are coloured grey. c, Local-resolution-filtered map of Mediator–PICwith the fitted structure. The inset shows a magnified view of the CAK module fitting into our density. d, Model-to-map FSCs, showing in blue the fit of the overall structure to the Mediator–PIC and in black the fit of the Mediator–Pol II stalk model to their corresponding maps.

Extended Data Fig. 4 Quality of cryo-EM densities.

Sections of focused-refined Mediator–stalk cryo-EM density overlaid with their respective atomic models. Densities are shown as a blue mesh, and sticks are shown for the model coloured as in Extended Fig. 3c.

Extended Data Fig. 5 Additional structural comparisons.

a, Comparison of the human Mediator–PIC structure (this study) with the free PIC structure25 reveals a different orientation of the Pol II RPB4–RPB7 stalk. The core PIC regions of the Mediator–PIC (in colour) and free PIC (in white) structures were superposed on the 10-subunit Pol II core. Mobile elements in the stalk are indicated and conformational changes between complexes are depicted by red arrows. b, Comparison of the yeast and human Mediator–PIC structures reveals a different relative orientation of the Mediator middle module. The human (in colour) and yeast9 (in white) Mediator–PIC structures were superposed on the well-conserved neck and fixed-jaw domains of the Mediator head module. Conformational changes of Mediator submodules are depicted by red arrows. The proximal tail region of human Mediator was omitted for clarity.

Extended Data Table 1 Cryo-EM data collection and processing

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-2.

Reporting Summary

Peer Review File

Video 1

Structure of the human Mediator-RNA polymerase II pre-initiation complex. Rotating views of the structure. For details refer to text.

Source data

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Rengachari, S., Schilbach, S., Aibara, S. et al. Structure of the human Mediator–RNA polymerase II pre-initiation complex. Nature 594, 129–133 (2021).

Download citation


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing