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

Contrast transfer function parameters for each micrograph were determined by Gctf v1.06(37) and particle selection were performed using auto-picking command in RELION-3.0-beta2(38), yielding 2,438,446 particle projections. The resulted particles were imported to cryoSPARC v2.4.2(39) and the following reference-free 2D classification was performed producing 1,834,912 particle projections for further processing. This subset of particle projections was subjected to two rounds of Hetero Refinement and two selected subsets containing 580,293 projections were used to obtain a map with resolution of 2.9 Ã… in cryoSPARC. This portion of particle projections were imported back to RELION-3.0-beta2 and subjected to 3D refinement. Another round of 3D classification with mask on the complex produced a subset of 130,386 particle projections for the final reconstruction. After consecutive rounds of 3D refinement and Bayesian polishing of 130,386 particle projections, the final map has an indicated global resolution of 2.5 Ã… at a Fourier shell correlation (FSC) of 0.143. Local resolution was determined using the Bsoft package with half maps as input maps (40) .