Hudson, BP, Quispe, J, Lara-González, S, Kim, Y, Berman, HM, Arnold, E, Ebright, RH and Lawson, CL (2009) Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc. Natl. Acad. Sci. U.S.A. 106:19830-5
We present the experimentally determined 3D structure of an intact activator-dependent transcription initiation complex comprising the Escherichia coli catabolite activator protein (CAP), RNA polymerase holoenzyme (RNAP), and a DNA fragment containing positions -78 to +20 of a Class I CAP-dependent promoter with a CAP site at position -61.5 and a premelted transcription bubble. A 20-A electron microscopy reconstruction was obtained by iterative projection-based matching of single particles visualized in carbon-sandwich negative stain and was fitted using atomic coordinate sets for CAP, RNAP, and DNA. The structure defines the organization of a Class I CAP-RNAP-promoter complex and supports previously proposed interactions of CAP with RNAP alpha subunit C-terminal domain (alphaCTD), interactions of alphaCTD with sigma(70) region 4, interactions of CAP and RNAP with promoter DNA, and phased-DNA-bend-dependent partial wrapping of DNA around the complex. The structure also reveals the positions and shapes of species-specific domains within the RNAP beta', beta, and sigma(70) subunits.
Base Sequence; Cyclic AMP Receptor Protein/chemistry; Cyclic AMP Receptor Protein/ultrastructure; DNA, Bacterial/chemistry; DNA, Bacterial/ultrastructure; DNA-Directed RNA Polymerases/chemistry; DNA-Directed RNA Polymerases/ultrastructure; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/ultrastructure; Macromolecular Substances/chemistry; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Promoter Regions, Genetic; Protein Structure, Tertiary; Protein Subunits/chemistry; Transcription, Genetic
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