CryoEM structure of the Nipah virus nucleocapsid assembly.

De-Sheng Ker,Alfred A Antson,Sandra J Greive,Huw T Jenkins,Félix A Rey

doi:10.1371/journal.ppat.1009740

Abstract

Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we report the first cryoEM structure for a Henipavirus RNA-bound nucleocapsid assembly, at 3.5 Å resolution. The helical assembly is stabilised by previously undefined N- and C-terminal segments, contributing to subunit-subunit interactions. RNA is wrapped around the nucleocapsid protein assembly with a periodicity of six nucleotides per protomer, in the "3-bases-in, 3-bases-out" conformation, with protein plasticity enabling non-sequence specific interactions. The structure reveals commonalities in RNA binding pockets and in the conformation of bound RNA, not only with members of the Paramyxoviridae family, but also with the evolutionarily distant Filoviridae Ebola virus. Significant structural differences with other Paramyxoviridae members are also observed, particularly in the position and length of the exposed α-helix, residues 123-139, which may serve as a valuable epitope for surveillance and diagnostics.

Highlights

Nipah virus (NiV) and the closely related Hendra virus are emerging zoonotic RNA viruses that cause a range of illnesses, from asymptomatic infections to atypical pneumonia and fatal encephalitis
We used cryo-electron microscopy to determine accurate three-dimensional structure for several different assemblies of the Nipah virus nucleocapsid protein, in particular a detailed structure for the complex of this protein with RNA. This structural information is important for understanding detailed molecular interactions driving and stabilizing the nucleocapsid assembly formation that are of fundamental importance for understanding similar processes in a large group of ssRNA viruses
Apart from highlighting structural similarities and differences with nucleocapsid proteins of other viruses of the Paramyxoviridae family, these data will inform the development of new antiviral approaches for the henipaviruses

Summary

Introduction

Nipah virus (NiV) and the closely related Hendra virus are emerging zoonotic RNA viruses that cause a range of illnesses, from asymptomatic infections to atypical pneumonia and fatal encephalitis. The NiV RNA genome is encapsidated by the nucleoprotein (N), forming a long helical nucleocapsid assembly[1]. This assembly safeguards the viral genome from degradation, and serves as a template for productive transcription of mRNA and replication of the nascent viral RNA genome by the viral RNA dependent RNA polymerase (RdRp)[6]. The newly synthesized viral RNA genome is encapsidated co-transcriptionally by nascently translated N protein, driving the formation of a helical nucleocapsid assembly, making the N protein one of the most abundant viral proteins produced during infection. RNA binding by the N protein to form the nucleocapsid, is an essential step in viral assembly and understanding this process would inform the development of antivirals. The N protein is a highly immunogenic antigen, partly due to its high abundance during infection, making it a vital tool for the serological surveillance required for diagnostic and epidemiological studies of new and historic outbreaks[10,11]

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Conclusion