biostudies-literatureHudson BPNCRR NIH HHSHoward Hughes Medical InstituteNIAID NIH HHSNIGMS NIH HHS19830-5https://www.ebi.ac.uk/biostudies/studies/S-EPMC2775702biostudies-literatureUnknown106(47)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.Proceedings of the National Academy of Sciences of the United States of AmericaThree-dimensional EM structure of an intact activator-dependent transcription initiation complex.PMC2775702RR022375AI72766R01 GM021589RR17573P41 RR017573GM21589GM41376R01 GM041376R37 GM041376S10 RR022375R01 AI072766Hudson BPBerman HMQuispe JEbright RHLara-Gonzalez SArnold EKim YLawson CLfalseThree-dimensional EM structure of an intact activator-dependent transcription initiation complex.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.2009-01-01T00:00:00Z2009 Nov2022-02-11T04:58:43.234Z2019-03-27T00:26:30ZS-EPMC27757021990388110.1073/pnas.0908782106