National Natural Science Foundation of China (NSFC)
81520108019
中国
National Natural Science Foundation of China (NSFC)
813300237
中国
Ministry of Science and Technology (MoST, China)
2017YFC0840300
中国
引用
ジャーナル: Science / 年: 2020 タイトル: Structure of the RNA-dependent RNA polymerase from COVID-19 virus. 著者: Yan Gao / Liming Yan / Yucen Huang / Fengjiang Liu / Yao Zhao / Lin Cao / Tao Wang / Qianqian Sun / Zhenhua Ming / Lianqi Zhang / Ji Ge / Litao Zheng / Ying Zhang / Haofeng Wang / Yan Zhu / ...著者: Yan Gao / Liming Yan / Yucen Huang / Fengjiang Liu / Yao Zhao / Lin Cao / Tao Wang / Qianqian Sun / Zhenhua Ming / Lianqi Zhang / Ji Ge / Litao Zheng / Ying Zhang / Haofeng Wang / Yan Zhu / Chen Zhu / Tianyu Hu / Tian Hua / Bing Zhang / Xiuna Yang / Jun Li / Haitao Yang / Zhijie Liu / Wenqing Xu / Luke W Guddat / Quan Wang / Zhiyong Lou / Zihe Rao / 要旨: A novel coronavirus [severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of ...A novel coronavirus [severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase [(RdRp), also named nsp12] is the central component of coronaviral replication and transcription machinery, and it appears to be a primary target for the antiviral drug remdesivir. We report the cryo-electron microscopy structure of COVID-19 virus full-length nsp12 in complex with cofactors nsp7 and nsp8 at 2.9-angstrom resolution. In addition to the conserved architecture of the polymerase core of the viral polymerase family, nsp12 possesses a newly identified β-hairpin domain at its N terminus. A comparative analysis model shows how remdesivir binds to this polymerase. The structure provides a basis for the design of new antiviral therapeutics that target viral RdRp.
全体 : SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors
全体
名称: SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors
要素
複合体: SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors
タンパク質・ペプチド: RNA-directed RNA polymerase
タンパク質・ペプチド: Non-structural protein 7
タンパク質・ペプチド: Non-structural protein 8
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超分子 #1: SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors
超分子
名称: SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: The bacterially expressed full-length SARS-CoV-2 nsp12 (residues S1-Q932) was incubated with nsp7 (residues S1-Q83) and nsp8 (residues A1-Q198), and the complex was then purified
由来(天然)
生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス)
選択した数: 2334248 詳細: The particles were automatically selected using blob pickier (diameter range from 100 angstroms to 150 angstroms)
CTF補正
ソフトウェア - 名称: cryoSPARC (ver. 2.9.1) ソフトウェア - 詳細: cryoSPARC was used to determine CTF correction. 詳細: The CTF correction was done by patch CTF correction.
初期モデル
モデルのタイプ: NONE / 詳細: The startup models were generated automatically.
最終 再構成
使用したクラス数: 1 / 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC (ver. 2.9.1) ソフトウェア - 詳細: cryoSPARC was used to do final reconstruction 詳細: The particle set was used to perform homogeneous refinement, yielding a resolution of 3.1-angstrom. After local refinement, the final resolution reached 2.9-angstrom. 使用した粒子像数: 110176
初期 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 2.9.1) ソフトウェア - 詳細: cryoSPARC was used to do initial angular assignment 詳細: The initial angle assignment was generated by Ab-initio reconstruction.
最終 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 2.9.1) ソフトウェア - 詳細: cryoSPARC was used to do final angular assignment. 詳細: The final angle assignment was non-uniform refinement.
最終 3次元分類
クラス数: 5 / 平均メンバー数/クラス: 183622 / ソフトウェア - 名称: cryoSPARC (ver. 2.9.1) ソフトウェア - 詳細: cryoSPARC was used to do final classification 詳細: The final 3D classification can distinguish one class matching complete complex.
After the corresponding amino acids were replaced with those from 2019-nCoV, the model was manually built in Coot with the guidance of the cryo-EM map, and in combination with real space refinement with Phenix.
精密化
空間: REAL / プロトコル: RIGID BODY FIT / 温度因子: 65 / 当てはまり具合の基準: correlation coefficient
得られたモデル
PDB-6m71: SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors