title: Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
abstract: 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.
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hudson
authors.forename: Joel
authors.initials: J
authors.lastname: Quispe
authors.forename: Samuel
authors.initials: S
authors.lastname: Lara-González
authors.forename: Younggyu
authors.initials: Y
authors.lastname: Kim
authors.forename: Helen M
authors.initials: HM
authors.lastname: Berman
authors.forename: Eddy
authors.initials: E
authors.lastname: Arnold
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
authors.forename: Catherine L
authors.initials: CL
authors.lastname: Lawson
mesh_terms: D001483:Base Sequence; D002373:Cyclic AMP Receptor Protein / Q000737:chemistry / Q000648:ultrastructure*; D004269:DNA, Bacterial / Q000737:chemistry / Q000648:ultrastructure*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000648:ultrastructure*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000648:ultrastructure*; D046911:Macromolecular Substances / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry; D014158:Transcription, Genetic
chemical_list: D002373:Cyclic AMP Receptor Protein; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D021122:Protein Subunits; D012321:DNA-Directed RNA Polymerases