Molecular architecture of the yeast Mediator complex

• DOI: 10.7554/elife.08719
• Publication Date: 2015-09-24T11:55:35Z
• Authors: Philip J Robinson; Michael J Trnka; Riccardo Pellarin; Charles H Greenberg; David A Bushnell; Ralph Davis; Alma L Burlingame; Andrej Sali; Roger D Kornberg
• Keywords: Models, Molecular; Biomedical and clinical sciences; MESH: Cross-Linking Reagents/metabolism; QH301-705.5; Science; MESH: Saccharomyces cerevisiae/chemistry*; S. cerevisiae; Saccharomyces cerevisiae; Crystallography, X-Ray; Models, Biological; Mass Spectrometry; 03 medical and health sciences; Models; biophysics; Genetics; structural biology; transcriptional regulation; Biology (General); mass spectrometry; MESH: Mass Spectrometry; 0303 health sciences; Crystallography; Mediator Complex; Q; Cryoelectron Microscopy; MESH: Models, Biological; R; Molecular; Health sciences; modeling; Biological Sciences; Biological; MESH: Crystallography, X-Ray; Biophysics and Structural Biology; [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]; Biological sciences; MESH: Mediator Complex/chemistry*; Cross-Linking Reagents; X-Ray; Medicine; RNA polymerase II; Biochemistry and Cell Biology; MESH: Cryoelectron Microscopy; MESH: Models, Molecular; cross-linking

The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex.