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	Stepwise Promoter Melting by Bacterial RNA Polymerase.
Journal, issue, pages	Mol Cell, Vol. 78, Issue 2, Page 275-288.e6, Year 2020
Publish date	Apr 16, 2020
Authors	James Chen / Courtney Chiu / Saumya Gopalkrishnan / Albert Y Chen / Paul Dominic B Olinares / Ruth M Saecker / Jared T Winkelman / Michael F Maloney / Brian T Chait / Wilma Ross / Richard L Gourse / Elizabeth A Campbell / Seth A Darst /
PubMed Abstract	Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into ...Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.
External links	Mol Cell / PubMed:32160514 / PubMed Central
Methods	EM (single particle)
Resolution	3.0 - 3.9 Å
Structure data	20460 6psq EMDB-20460, PDB-6psq: Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter Method: EM (single particle) / Resolution: 3.4 Å 20461 6psr EMDB-20461, PDB-6psr: Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1) with TraR and rpsT P2 promoter Method: EM (single particle) / Resolution: 3.4 Å 20462 6pss EMDB-20462, PDB-6pss: Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5a) with TraR and mutant rpsT P2 promoter Method: EM (single particle) / Resolution: 3.5 Å 20463 6pst EMDB-20463, PDB-6pst: Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5b) with TraR and mutant rpsT P2 promoter Method: EM (single particle) / Resolution: 3.0 Å 20464 6psu EMDB-20464, PDB-6psu: Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and rpsT P2 promoter Method: EM (single particle) / Resolution: 3.9 Å 20465 6psv EMDB-20465, PDB-6psv: Escherichia coli RNA polymerase promoter unwinding intermediate (TpreRPo) with TraR and rpsT P2 promoter Method: EM (single particle) / Resolution: 3.5 Å 20466 6psw EMDB-20466, PDB-6psw: Escherichia coli RNA polymerase promoter unwinding intermediate (TRPo) with TraR and rpsT P2 promoter Method: EM (single particle) / Resolution: 3.7 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-1N7: CHAPSO / detergent*YM / CHAPS detergent
Source	escherichia coli (E. coli)
Keywords	transcription/dna / TRANSCRIPTION / transcription-dna complex