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	Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.
Journal, issue, pages	Nat Commun, Vol. 11, Issue 1, Page 6419, Year 2020
Publish date	Dec 18, 2020
Authors	Tomáš Kouba / Tomáš Koval' / Petra Sudzinová / Jiří Pospíšil / Barbora Brezovská / Jarmila Hnilicová / Hana Šanderová / Martina Janoušková / Michaela Šiková / Petr Halada / Michal Sýkora / Ivan Barvík / Jiří Nováček / Mária Trundová / Jarmila Dušková / Tereza Skálová / URee Chon / Katsuhiko S Murakami / Jan Dohnálek / Libor Krásný /
PubMed Abstract	RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism ...RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids.
External links	Nat Commun / PubMed:33339823 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2 - 3.36 Å
Structure data	10996 6yxu EMDB-10996, PDB-6yxu: Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State I, primary channel engaged Method: EM (single particle) / Resolution: 3.08 Å 11004 6yys EMDB-11004, PDB-6yys: Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interfering Method: EM (single particle) / Resolution: 3.08 Å 11026 6z11 EMDB-11026, PDB-6z11: Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State III, primary channel dis-engaged and active site interfering Method: EM (single particle) / Resolution: 3.36 Å PDB-6vsx: X-ray crystal structure of the C-terminal domain of Bacillus subtilis RNA polymerase binding helicase HelD Method: X-RAY DIFFRACTION / Resolution: 2.0 Å
Chemicals	ChemComp-PO4: PHOSPHATE ION / Phosphate ChemComp-HOH: WATER / Water ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry
Source	mycolicibacterium smegmatis mc2 155 (bacteria) bacillus subtilis (bacteria)
Keywords	TRANSCRIPTION / RNA polymerase / Helicase / transcription cycle helicase-like protein RNA polymerase / trasncription / transcription cycle helicase-like protein RNA polymerase transcription