3IYD

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Summary for 3IYD

• Entry DOI: 10.2210/pdb3iyd/pdb
• EMDB information: 5127
• Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit omega, ... (9 entities in total)
• Functional Keywords: transcription, initiation, class i, activator, rna polymerase, holoenzyme, sigma70, open complex, cap, crp, camp-dependent, dna, prokaryotic, dna-directed rna polymerase, nucleotidyltransferase, transferase, dna-binding, sigma factor, transcription regulation, camp, camp-binding, nucleotide-binding, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 10
• Total formula weight: 568637.03

Authors

Hudson, B.P.,Quispe, J.,Lara, S.,Kim, Y.,Berman, H.,Arnold, E.,Ebright, R.H.,Lawson, C.L. (deposition date: 2009-08-01, release date: 2009-11-10, Last modification date: 2024-02-21)

Primary citation

Hudson, B.P.,Quispe, J.,Lara-Gonzalez, S.,Kim, Y.,Berman, H.M.,Arnold, E.,Ebright, R.H.,Lawson, C.L.
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
Proc.Natl.Acad.Sci.USA, 106:19830-19835, 2009

PubMed 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.

PubMed: 19903881
DOI: 10.1073/pnas.0908782106

Experimental method

ELECTRON MICROSCOPY (19.8 Å)