Molecule of the Month: Mediator

Mediator integrates regulatory information to decide when genes need to be transcribed.

Pre-initiation complex of Mediator, RNA polymerase II, DNA and general transcription factors.
Pre-initiation complex of Mediator, RNA polymerase II, DNA and general transcription factors.
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Remarkably, our cells only need about 20,000 different types of proteins to manage all of the tasks we need throughout our lives. The trick, of course, is to control when and where these proteins are built and used, so that, for example, muscle cells have plenty of myosin and nerve cells have the appropriate combination of ion channels, transporters, and receptors. Most of these choices are made at the level of transcription. Cells carefully control when messenger RNA molecules are transcribed by RNA polymerase II from particular genes, and used to build proteins. Over 1600 side-specific DNA binding regulatory proteins, termed transcription factors, work together to make these decisions, monitoring the current state of the cell and deciding if action is needed. Mediator, a large protein complex composed of about 30 different protein chains, integrates these many inputs, and mobilizes RNA polymerase II when and where in the body a particular protein is needed.

Getting Started

The structure shown here, from PDB ID 7enc, is a “pre-initiation complex” poised to start transcription. This complex includes eukaryotic Mediator and RNA polymerase II, the major RNA polymerase that builds messenger RNAs based on information encoded in the genome. The pre-initiation complex also includes a collection of general transcription factors (described below) that perform the necessary tasks of recognizing the transcription start site of genes, separating the two strands of the DNA double helix, and facilitating transcription initiation by RNA polymerase II. However, currently available structures of Mediator don't show an important function of the complex. Mediator also interacts with hundreds of other transcription factors that decide which genes need to be transcribed. The structural details of these interactions are still largely a mystery.

Interaction at a Distance

Most of our transcription factors bind to regulatory regions in DNA that are separate from the initiation site, such as promoter-proximal and distal enhancer elements. Mediator interacts with these transcription factors and helps decide when a pre-initiation complex needs to be built. Researchers have uncovered many interesting aspects of these interactions. Several of the subunits in Mediator are important for the interactions, particularly subunits in the fork-shaped tail seen at the right in the illustration. Mediator can interact with transcription factors at regulatory sites that are far away in the genome, bridging distal enhancers and the pre-initiation complex. To complicate matters further, it is becoming clear that some of these interactions may involve intrinsically disordered segments of Mediator subunits or transcription factors, perhaps forming phase-separated droplets that bring Mediator together with regulatory proteins.

The pre-initiation complex viewed from the opposite side, showing the location of the general transcription factors.
The pre-initiation complex viewed from the opposite side, showing the location of the general transcription factors.
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General Transcription Factors

This structure reveals the arrangement of general transcription factors that cradle RNA polymerase in the pre-initiation complex. TATA-binding protein (TBP, part of TFIID) is the central player that gets the process started. It binds to a distinctive AT-rich sequence and functions as a molecular saddle that sharply bends the DNA. TFIIA and TFIIB interact with surrounding regions of the DNA and, along with TFIIF, assist with positioning of RNA polymerase II at the transcription start site. TFIIE, TFIIH, and other TFIID subunits bring additional functionality to the complex. In particular, part of TFIIH is a translocase that separates the two strands of DNA in preparation for transcription, and the CAK module of TFIIH adds phosphate groups to the long tail of RNA polymerase II, sending the signal that it is time to get started with mRNA synthesis.

RNA polymerase II with the heptad repeats of RPB1 shown in shades of magenta.
RNA polymerase II with the heptad repeats of RPB1 shown in shades of magenta.
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Wagging Tails

The largest subunit of RNA polymerase II, termed RPB1, has a long tail that does not adopt a folded structure (shown here from PDB ID 5iyd combined with computed structure model AF-P24928F1). It includes 52 repeats of a distinctive serine-rich protein sequence (termed the heptad repeat). In each repeat, the fifth serine is phosphorylated by the CAK module of TFIIH. When the tail is highly phosphorylated, the interaction between Mediator and RNA polymerase II is weakened, allowing RNA polymerase II to proceed with mRNA synthesis. The phosphorylated chain also recruits enzymes that build the unusual chemical cap that protects the front end of the mRNA from degradation.

Exploring the Structure

Mediator Flexibility

Mediator must interact with many different proteins in its role in integrating regulatory signals. It does this in part by being flexible, to accommodate the structural needs of its many partners. We can see some of this flexibility by comparing three different structures: PDB IDs 6w1s and 7enj of Mediator alone, and a pre-initiation complex in PDB ID 7lbm. In addition, when you explore these structures, you’ll find that many portions of the Mediator proteins are not included in the structures. These stretches are thought to be intrinsically disordered, leaving them free to reach out and interact with surrounding partners. To explore these structures in more detail, use the tab above to view an interactive JSmol.

Topics for Further Discussion

  1. A nearby nucleosome may also be important for the regulatory role of Mediator. You can explore this in PDB ID 8gxs.
  2. You can use the Protein Feature View to find portions of the chain that are not resolved in the atomic structures. For example, look at the end of the chain of RPB to see the repeated heptad sequence YSPTSPS.


  1. Malik, S., Roeder, R. G. (2023) Regulation of RNA polymerase II pre-initiation complex by its associated coactivators. Nat Rev Genetics 24, 767-782.
  2. Richter, W. F., Nayak, S., Iwasa, J., Taatjes, D. J. (2022) The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 23, 732-749.
  3. 7lbm: Abdella, R., Talyzina, A., Chen, S., Inouye, C.J., Tjian, R., He, Y. (2021) Structure of the human Mediator-bound transcription preinitiation complex. Science 372: 52-56.
  4. 7enc, 7enj: Chen, X., Yin, X., Li, J., Wu, Z., Qi, Y., Wang, X., Liu, W., Xu, Y. (2021) Structures of the human Mediator and Mediator-bound preinitiation complex. Science 372, eabg0635.
  5. 6w1s: El Khattabi, L., Zhao, H., Kalchschmidt, J., Young, N., Jung, S., Van Blerkom, P., Kieffer-Kwon, P., Kieffer-Kwon, K.R., Park, S., Wang, X., Krebs, J., Tripathi, S., Sakabe, N., Sobreira, D.R., Huang, S.C., Rao, S.S.P., Pruett, N., Chauss, D., Sadler, E., Lopez, A., Nobrega, M.A., Aiden, E.L., Asturias, F.J., Casellas, R. (2019) A pliable Mediator acts as a functional rather than an architectural bridge between promoters and enhancers. Cell 178: 1145-1158.e20.
  6. Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., Weirauch, M. T. (2018) The human transcription factors. Cell 172, 650-665.
  7. 5iyd: He, Y., Yan, C., Fang, J., Inouye, C., Tjian, R., Ivanov, I., Nogales, E.(2016) Near-atomic resolution visualization of human transcription promoter opening. Nature 533: 359-365.

January 2024, David Goodsell
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More