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	Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106.
Journal, issue, pages	Cell Rep, Vol. 42, Issue 1, Page 111901, Year 2023
Publish date	Jan 31, 2023
Authors	Tomas Kouba / Anna Dubankova / Petra Drncova / Elisa Donati / Pietro Vidossich / Valentina Speranzini / Alex Pflug / Johanna Huchting / Chris Meier / Marco De Vivo / Stephen Cusack /
PubMed Abstract	The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although ...The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although dispersed, single pseudo-base incorporation is mutagenic, consecutive incorporation causes polymerase stalling and chain termination. Using a template encoding single and then consecutive T1106 incorporation four nucleotides later, we obtained a cryogenic electron microscopy structure of stalled influenza A/H7N9 polymerase. This shows that the entire product-template duplex backtracks by 5 nt, bringing the singly incorporated T1106 to the +1 position, where it forms an unexpected T1106:U wobble base pair. Similar structures show that influenza B polymerase also backtracks after consecutive T1106 incorporation, regardless of whether prior single incorporation has occurred. These results give insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogs. Consecutive incorporation destabilizes the proximal end of the product-template duplex, promoting irreversible backtracking to a more energetically favorable overall configuration.
External links	Cell Rep / PubMed:36596301
Methods	EM (single particle)
Resolution	2.34 - 3.12 Å
Structure data	14144 7qtl EMDB-14144, PDB-7qtl: Influenza A/H7N9 polymerase elongation complex Method: EM (single particle) / Resolution: 2.48 Å 14222 7r0e EMDB-14222, PDB-7r0e: Early transcription elongation state of influenza A/H7N9 polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the +1 position Method: EM (single particle) / Resolution: 2.51 Å 14240 7r1f EMDB-14240, PDB-7r1f: Early transcription elongation state of influenza B polymerase backtracked due to double incoproation of nucleotide analogue T1106 Method: EM (single particle) / Resolution: 2.58 Å 14857 7zpl EMDB-14857, PDB-7zpl: Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook Method: EM (single particle) / Resolution: 3.12 Å 14858 7zpm EMDB-14858, PDB-7zpm: Influenza A/H7N9 polymerase apo-protein dimer complex Method: EM (single particle) / Resolution: 2.81 Å 15984 8bdr EMDB-15984, PDB-8bdr: Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the U +1 position Method: EM (single particle) / Resolution: 2.7 Å 15996 8be0 EMDB-15996, PDB-8be0: Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position Method: EM (single particle) / Resolution: 2.34 Å 16006 8bek EMDB-16006, PDB-8bek: Early transcription elongation state of influenza A/H7N9 backtracked polymerase with singly incoporated T1106 at the U +1 position Method: EM (single particle) / Resolution: 2.86 Å 16013 8bf5 EMDB-16013, PDB-8bf5: Early transcription elongation state of influenza A/H7N9 polymerase stalled with incoming GTP analogue Method: EM (single particle) / Resolution: 2.96 Å
Chemicals	ChemComp-2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine ChemComp-MG: Unknown entry ChemComp-GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE ChemComp-HOH: WATER / Water ChemComp-G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM
Source	influenza a virus (a/zhejiang/dtid-zju01/2013(h7n9)) influenza a virus influenza b virus (b/memphis/13/2003) influenza b virus influenza b virus (b/acre/117700/2012) influenza b virus (b/kaliningrad/rii06/2012)
Keywords	VIRAL PROTEIN / Influenza / viral RNA-dependent RNA polymerase; cap-dependent transcription / viral RNA-dependent RNA polymerase; antiviral drug; nucleoside analogue; T705 (favipiravir); T1106; cap-dependent transcription; backtracking; / H7N9 / viral RNA-dependent RNA polymerase / viral RNA-dependent RNA polymerase; / nucleoside analogue