Structure of the Ebola virus polymerase complex

Nature. 2022 Oct;610(7931):394-401. doi: 10.1038/s41586-022-05271-2.

Bin Yuan ^# ¹ ², Qi Peng ^# ¹, Jinlong Cheng ¹, Min Wang ¹, Jin Zhong ² ³, Jianxun Qi ¹, George F Gao ⁴ ⁵ ⁶ ⁷, Yi Shi ⁸ ⁹ ¹⁰ ¹¹

Affiliations

1 CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
2 Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
3 CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
4 CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.
5 Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.
6 Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.
7 Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China. gaof@im.ac.cn.
8 CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.
9 Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.
10 Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.
11 Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China. shiyi@im.ac.cn.
# Contributed equally.

PMID: 36171293 DOI: 10.1038/s41586-022-05271-2

Abstract

Filoviruses, including Ebola virus, pose an increasing threat to the public health. Although two therapeutic monoclonal Antibodies have been approved to treat the Ebola virus disease^1,2, there are no approved broadly reactive drugs to control diverse Filovirus infection. Filovirus has a large polymerase (L) protein and the cofactor viral protein 35 (VP35), which constitute the basic functional unit responsible for virus genome RNA synthesis³. Owing to its conservation, the L-VP35 polymerase complex is a promising target for broadly reactive Antiviral drugs. Here we determined the structure of Ebola virus L protein in complex with tetrameric VP35 using cryo-electron microscopy (state 1). Structural analysis revealed that Ebola virus L possesses a filovirus-specific insertion element that is essential for RNA synthesis, and that VP35 interacts extensively with the N-terminal region of L by three protomers of the VP35 tetramer. Notably, we captured the complex structure in a second conformation with the unambiguous priming loop and supporting helix away from polymerase active site (state 2). Moreover, we demonstrated that the century-old drug suramin could inhibit the activity of the Ebola virus polymerase in an enzymatic assay. The structure of the L-VP35-suramin complex reveals that suramin can bind at the highly conserved NTP entry channel to prevent substrates from entering the active site. These findings reveal the mechanism of Ebola virus replication and may guide the development of more powerful anti-filovirus drugs.

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