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	A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.
Journal, issue, pages	Cell, Vol. 185, Issue 23, Page 4347-4360.e17, Year 2022
Publish date	Nov 10, 2022
Authors	Liming Yan / Yucen Huang / Ji Ge / Zhenyu Liu / Pengchi Lu / Bo Huang / Shan Gao / Junbo Wang / Liping Tan / Sihan Ye / Fengxi Yu / Weiqi Lan / Shiya Xu / Feng Zhou / Lei Shi / Luke W Guddat / Yan Gao / Zihe Rao / Zhiyong Lou /
PubMed Abstract	Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The ...Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.
External links	Cell / PubMed:36335936 / PubMed Central
Methods	EM (single particle)
Resolution	2.64 - 3.8 Å
Structure data	34302 8gw1 EMDB-34302, PDB-8gw1: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Method: EM (single particle) / Resolution: 3.31 Å 34308 8gwb EMDB-34308: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors PDB-8gwb: SARS-CoV-2 E-RTC complex with RNA-nsp9 Method: EM (single particle) / Resolution: 2.75 Å 34310 8gwe EMDB-34310: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors PDB-8gwe: SARS-CoV-2 E-RTC complex with RNA-nsp9 and GMPPNP Method: EM (single particle) / Resolution: 2.66 Å 34311 8gwf EMDB-34311, PDB-8gwf: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Method: EM (single particle) / Resolution: 3.39 Å 34312 8gwg EMDB-34312, PDB-8gwg: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Method: EM (single particle) / Resolution: 3.37 Å 34313 8gwi EMDB-34313, PDB-8gwi: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Method: EM (single particle) / Resolution: 3.18 Å 34314 8gwk EMDB-34314, PDB-8gwk: SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP Method: EM (single particle) / Resolution: 2.72 Å 34316 8gwm EMDB-34316, PDB-8gwm: SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP Method: EM (single particle) / Resolution: 2.64 Å 34317 8gwn EMDB-34317: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors PDB-8gwn: A mechanism for SARS-CoV-2 RNA capping and its inhibitor of AT-527 Method: EM (single particle) / Resolution: 3.38 Å 34318 8gwo EMDB-34318, PDB-8gwo: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Method: EM (single particle) / Resolution: 3.8 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MN: Unknown entry ChemComp-U5P: URIDINE-5'-MONOPHOSPHATE ChemComp-HOH: WATER ChemComp-GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM ChemComp-F86: [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate / medication, antivirusYM ChemComp-6GS*: 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate)
Source	severe acute respiratory syndrome coronavirus 2 synthetic construct (others)
Keywords	VIRAL PROTEIN / SARS-CoV-2 / capping / nucleotide analogue inhibitor / cryo-EM / VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR complex