Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural origins of RNA polymerase open promoter complex stability.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 118, Issue 40, Year 2021
Publish date	Oct 5, 2021
Authors	Ruth M Saecker / James Chen / Courtney E Chiu / Brandon Malone / Johanna Sotiris / Mark Ebrahim / Laura Y Yen / Edward T Eng / Seth A Darst /
PubMed Abstract	The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In , promoter DNA sequence fundamentally determines how fast the ...The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In , promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms "open" complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo, but their structural origins remain largely unknown. Here, we use cryoelectron microscopy to determine the structures of RPo formed de novo at three promoters with widely differing lifetimes at 37 °C: λP (t ∼10 h), T7A1 (t ∼4 min), and a point mutant in λP (λP) (t ∼2 h). Two distinct RPo conformers are populated at λP, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand "scrunches" inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.
External links	Proc Natl Acad Sci U S A / PubMed:34599106 / PubMed Central
Methods	EM (single particle)
Resolution	2.9 - 3.7 Å
Structure data	23892 7mkd EMDB-23892, PDB-7mkd: Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 1) Method: EM (single particle) / Resolution: 3.2 Å 23893 7mke EMDB-23893, PDB-7mke: Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 2) Method: EM (single particle) / Resolution: 3.7 Å 23895 7mki EMDB-23895, PDB-7mki: Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR (-5G to C) promoter DNA Method: EM (single particle) / Resolution: 3.5 Å 23897 7mkj EMDB-23897, PDB-7mkj: Cryo-EM structure of Escherichia coli RNA polymerase bound to T7A1 promoter DNA Method: EM (single particle) / Resolution: 2.9 Å
Chemicals	ChemComp-1N7: CHAPSO / detergentYM ChemComp-MG: Unknown entry ChemComp-ZN*: Unknown entry
Source	escherichia coli (E. coli) escherichia virus lambda escherichia phage t7 (virus)
Keywords	TRANSCRIPTION/DNA / DNA-dependent RNA polymerase / transcription / DNA promoter / open complex / TRANSCRIPTION-DNA complex