Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2

Qi Peng; Ruchao Peng; Bin Yuan; Jingru Zhao; Min Wang; Xixi Wang; Qian Wang; Yan Sun; Zheng Fan; Jianxun Qi; George F Gao; Yi Shi

doi:10.1016/j.celrep.2020.107774

Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2

Cell Rep. 2020 Jun 16;31(11):107774. doi: 10.1016/j.celrep.2020.107774. Epub 2020 May 30.

Authors

Qi Peng¹, Ruchao Peng¹, Bin Yuan², Jingru Zhao², Min Wang¹, Xixi Wang¹, Qian Wang², Yan Sun³, Zheng Fan¹, Jianxun Qi⁴, George F Gao⁴, Yi Shi⁵

Affiliations

¹ CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
² CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China.
³ Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China.
⁴ CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China.
⁵ CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing General Hospital, University of the Chinese Academy of Sciences, Chongqing 400013, China; College of Basic Medicine, Jilin University, Changchun, Jilin 130021, China. Electronic address: shiyi@im.ac.cn.

Abstract

The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused a huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus (SARS-CoV-2). The viral polymerase is a promising antiviral target. Here, we describe the near-atomic-resolution structure of the SARS-CoV-2 polymerase complex consisting of the nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases and suggests a mechanism of activation by cofactors. Biochemical studies reveal reduced activity of the core polymerase complex and lower thermostability of individual subunits of SARS-CoV-2 compared with SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate adaptation of SARS-CoV-2 toward humans with a relatively lower body temperature than the natural bat hosts.

Keywords: RNA synthesis; SARS-CoV-2; cofactors; cryo-EM; non-structural proteins; polymerase.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Substitution
Betacoronavirus / enzymology*
Coronavirus RNA-Dependent RNA Polymerase
Cryoelectron Microscopy*
Escherichia coli / genetics
Evolution, Molecular
Models, Molecular
Multiprotein Complexes / chemistry
RNA-Dependent RNA Polymerase / chemistry*
RNA-Dependent RNA Polymerase / metabolism
SARS-CoV-2
Severe acute respiratory syndrome-related coronavirus / enzymology
Viral Nonstructural Proteins / chemistry*
Viral Nonstructural Proteins / metabolism

Substances

Multiprotein Complexes
NS8 protein, SARS-CoV-2
Viral Nonstructural Proteins
Coronavirus RNA-Dependent RNA Polymerase
NSP12 protein, SARS-CoV-2
NSP7 protein, SARS-CoV-2
RNA-Dependent RNA Polymerase