Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir

Wanchao Yin; Chunyou Mao; Xiaodong Luan; Dan-Dan Shen; Qingya Shen; Haixia Su; Xiaoxi Wang; Fulai Zhou; Wenfeng Zhao; Minqi Gao; Shenghai Chang; Yuan-Chao Xie; Guanghui Tian; He-Wei Jiang; Sheng-Ce Tao; Jingshan Shen; Yi Jiang; Hualiang Jiang; Yechun Xu; Shuyang Zhang; Yan Zhang; H. Eric Xu

A, Schematic diagram for the components of the active RdRp complex, containing nsp12, nsp7 and nsp8, with the nsp12 displayed in domain organization. The polymerase motif (A-G) and βhairpin unique to the SARS-CoV-2 are highlighted. B, Sequence of RNA duplex with a 5' U10 overhang as template used for extension reactions and RdRp-RNA complex assembly. C, The recombinant RdRp complex shows polymerase activity in vitro. The primer strand is labeled with fluorescence at the 5' end. D, Elongation of partial RNA duplex by the purified RdRp complex is inhibited by RTP. A-B, Cryo-EM density map (A) and structure (B) of the nsp12-nsp7-nsp8 complex in apo state are shown in two views, colored according to Fig.1A . C, The conserved metal binding motifs composed by H295-C301-C306-C310 and C487-H642-C645-C646 are highlighted in the apo structure rendered in ribbon. To the right, the coordinate details of the zinc-binding residues are shown in stick against the cryo-EM map which is rendered in grey surface. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint A, A superimposition of three complex structures based on the alignment of RNA. Only the molecular surface of SARS-CoV-2 RdRp is shown. The bound RNA in SARS-CoV-2, HCV, and poliovirus RdRp is colored green, magenta and grey, respectively. B-D, The RNA and the bound ligand in the RdRp-RNA complex of HCV (B), SARS-CoV-2 (C) and poliovirus (D) are shown as cartoon and sticks, respectively. The base paired with the bound ligand and a serine nearby are shown as sticks too. Figure S8 . Superimpose of the seven conserved motifs between the apo structure and the RNA bond complex structure. Motifs A to G of the apo RdRp complex are shown as ribbon and colored as grey. Motifs A to G of the RNA bound RdRp complex are colored as tan, green, blue, orange, yellow, dark red and purple, respectively. Remdesivir and key residues of the active site are show in sticks, with the two Mg2+ are shown as sphere and colored as green. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint 23 Figure S2 . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint 24 Figure S3 . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint 25 Figure S4 . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint 26 Figure S5 . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.032763 doi: bioRxiv preprint 27 Figure S6 . CC-BY-NC 4.0 International license autho