EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.
ジャーナル・号・ページ	Cell, Vol. 185, Issue 23, Page 4347-4360.e17, Year 2022
掲載日	2022年11月10日
著者	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 要旨	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.
リンク	Cell / PubMed:36335936 / PubMed Central
手法	EM (単粒子)
解像度	2.64 - 3.8 Å
構造データ	34302 8gw1 EMDB-34302, PDB-8gw1: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 2.66 Å 34311 8gwf EMDB-34311, PDB-8gwf: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors 手法: EM (単粒子) / 解像度: 3.39 Å 34312 8gwg EMDB-34312, PDB-8gwg: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors 手法: EM (単粒子) / 解像度: 3.37 Å 34313 8gwi EMDB-34313, PDB-8gwi: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors 手法: EM (単粒子) / 解像度: 3.18 Å 34314 8gwk EMDB-34314, PDB-8gwk: SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP 手法: EM (単粒子) / 解像度: 2.72 Å 34316 8gwm EMDB-34316, PDB-8gwm: SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 3.38 Å 34318 8gwo EMDB-34318, PDB-8gwo: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors 手法: EM (単粒子) / 解像度: 3.8 Å
化合物	ChemComp-ZN: Unknown entry ChemComp-MN: Unknown entry ChemComp-U5P: URIDINE-5'-MONOPHOSPHATE / UMP / ウリジル酸 ChemComp-HOH: WATER / 水 ChemComp-GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Gpp(NH)p / GppNHp, GMPPNP, エネルギー貯蔵分子類似体YM / 5'-Guanylyl imidodiphosphate ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP / GTP, エネルギー貯蔵分子YM / グアノシン三リン酸 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 / 薬剤, 抗ウイルス剤YM / レムデシビル ChemComp-6GS*: 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate)
由来	severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2) synthetic construct (人工物)
キーワード	VIRAL PROTEIN (ウイルスタンパク質) / SARS-CoV-2 (SARSコロナウイルス2) / capping / nucleotide analogue inhibitor / cryo-EM (低温電子顕微鏡法) / VIRAL PROTEIN/INHIBITOR (ウイルス性) / VIRAL PROTEIN-INHIBITOR complex (ウイルス性)