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	Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 29, Issue 3, Page 250-260, Year 2022
Publish date	Mar 8, 2022
Authors	James Chen / Qi Wang / Brandon Malone / Eliza Llewellyn / Yakov Pechersky / Kashyap Maruthi / Ed T Eng / Jason K Perry / Elizabeth A Campbell / David E Shaw / Seth A Darst /
PubMed Abstract	The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA-dependent RNA ...The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA-dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex or RTC) associated with two copies of nsp13 (nsp13-RTC). One copy of nsp13 interacts with the template-RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backward on the RNA template (backtracking), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of nsp13. Here we use cryogenic-electron microscopy and molecular dynamics simulations to analyze the nsp13-RTC, revealing four distinct conformational states of the helicases. The results indicate a mechanism for the nsp13-RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis or backtracking in response to stimuli at the RdRp active site.
External links	Nat Struct Mol Biol / PubMed:35260847 / PubMed Central
Methods	EM (single particle)
Resolution	2.91 - 3.6 Å
Structure data	24426 7rdx EMDB-24426, PDB-7rdx: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - open class Method: EM (single particle) / Resolution: 3.1 Å 24427 7rdy EMDB-24427, PDB-7rdy: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - engaged class Method: EM (single particle) / Resolution: 3.1 Å 24428 7rdz EMDB-24428, PDB-7rdz: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - apo class Method: EM (single particle) / Resolution: 3.6 Å 24429 7re0 EMDB-24429, PDB-7re0: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - swiveled class Method: EM (single particle) / Resolution: 3.5 Å 24430 7re1 EMDB-24430, PDB-7re1: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC (composite) Method: EM (single particle) / Resolution: 2.91 Å 24431 7re2 EMDB-24431, PDB-7re2: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(1)-RTC Method: EM (single particle) / Resolution: 3.17 Å 24432 7re3 EMDB-24432, PDB-7re3: SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC dimer Method: EM (single particle) / Resolution: 3.33 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-1N7: CHAPSO / detergentYM / CHAPS detergent ChemComp-AF3: ALUMINUM FLUORIDE / Aluminium fluoride ChemComp-HOH: WATER / Water
Source	severe acute respiratory syndrome coronavirus 2 synthetic construct (others)
Keywords	REPLICATION/TRANSCRIPTION / RNA-dependent RNA polymerase / viral replication-transcription complex / transcription / viral proteins / REPLICATION-TRANSCRIPTION complex