To build the structure of SARS-CoV-2 Cap(0)-RTC complex, we started with the model of the SARS-CoV-2 nsp12 and nsp7-8 complex (PDB: 7BTF), SARS-CoV-2 nsp13 (PDB: 6ZSL), nsp9 (PDB: 6W9Q) and nsp10/nsp14 (PDB: 6C8S). These were individually placed and rigid-body fitted into the cryo-EM map using UCSF Chimera(Pettersen et al., 2004). The model was manually built in Coot(Emsley et al., 2010) with the guidance of the cryo-EM map, and with real space refinement using Phenix(Afonine et al., 2018). The data validation statistics are shown in Table S1.

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