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PMID: 26483468 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Structure of an RNA polymerase II preinitiation complex.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 112 ·No. 44 ·2015-11-03 ·Pages 13543-8

Murakami K, Tsai KL, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD

Abstract

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.

Keywords
cryo-EM general transcription factors transcription yeast
MeSH Terms
Cryoelectron Microscopy DNA/chemistry,genetics,metabolism,ultrastructure Humans Models, Molecular Multiprotein Complexes/chemistry,metabolism,ultrastructure Nucleic Acid Conformation Promoter Regions, Genetic/genetics Protein Binding Protein Isoforms/chemistry,metabolism,ultrastructure Protein Structure, Tertiary Protein Subunits/chemistry,metabolism RNA Polymerase II/chemistry,metabolism,ultrastructure Saccharomyces cerevisiae/genetics,metabolism TATA Box/genetics Transcription Factors/chemistry,metabolism,ultrastructure Transcription Factors, TFII/chemistry,metabolism,ultrastructure Transcription, Genetic
Chemicals
Multiprotein Complexes Protein Isoforms Protein Subunits Transcription Factors Transcription Factors, TFII DNA RNA Polymerase II
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Murakami Kenji
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;
Tsai Kuang-Lei
Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA 92037;
Kalisman Nir
Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
Bushnell David A
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
Asturias Francisco J
Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA 92037;
Kornberg Roger D
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; kornberg@stanford.edu.
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
1091-6490
DOI
10.1073/pnas.1518255112
Email
kornberg@stanford.edu
Published
2015-11-03
Epub
2015-00-19
Pages
13543-8
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC4640751
Subset
IM
Grants
NIGMS NIH HHS · GM49985 · United States
NCRR NIH HHS · S10 RR028096 · United States
NIGMS NIH HHS · R01 GM067167 · United States
NIGMS NIH HHS · GM067167 · United States
NIGMS NIH HHS · R01 GM049985 · United States
NIAID NIH HHS · R01 AI021144 · United States
NIAID NIH HHS · AI21144 · United States
NCRR NIH HHS · S10RR028096 · United States
External Links
PubMed source DOI: 10.1073/pnas.1518255112 PMC Full Text View journal details
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