Structure of an RNA polymerase II preinitiation complex.
The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
Kenji
K
Murakami
Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA 92037;
Kuang-Lei
KL
Tsai
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
Nir
N
Kalisman
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
David A
DA
Bushnell
Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA 92037;
Francisco J
FJ
Asturias
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; kornberg@stanford.edu.
Roger D
RD
Kornberg
D020285:Cryoelectron Microscopy; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D006801:Humans; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D020033:Protein Isoforms / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D012319:RNA Polymerase II / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D016385:TATA Box / Q000235:genetics; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D019473:Transcription Factors, TFII / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D014158:Transcription, Genetic
D046912:Multiprotein Complexes; D020033:Protein Isoforms; D021122:Protein Subunits; D014157:Transcription Factors; D019473:Transcription Factors, TFII; D004247:DNA; D012319:RNA Polymerase II
cryo-EM; general transcription factors; transcription; yeast