Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization

S Saif Hasan,Chengqun Sun,Arthur S Kim,Yasunori Watanabe,Chun-Liang Chen,Thomas Klose,Geeta Buda,Max Crispin,Michael S Diamond,William B Klimstra,Michael G Rossmann

doi:10.1016/j.celrep.2018.11.067

Abstract

SummaryAlphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid dissociation from envelope proteins. The EEEV capsid structure showed a viral RNA genome binding site adjacent to a ribosome binding site for viral genome translation following genome release. Using five Fab-EEEV complexes derived from neutralizing antibodies, our investigation provides insights into EEEV host cell interactions and protective epitopes relevant to vaccine design.

Highlights

Alphaviruses are arthropod-transmitted enveloped pathogens that cause epidemics in humans and other vertebrate animals (Jose et al, 2009; Schwartz and Albert, 2010; Strauss and Strauss, 1994)
The icosahedral shell of alphaviruses consists of an outer layer of trans-membrane envelope E1 and E2 proteins and an inner capsid layer separated by a host-derived membrane
Previous cryoelectron microscopy studies of chikungunya (CHIKV), Semliki Forest (SFV), Sindbis (SINV), Ross River (RRV), Venezuelan (VEEV), and western equine encephalitis (WEEV) viruses have shown that the E1 and E2 proteins are organized into 20 icosahedral 3-fold and 60 quasi-3-fold trimeric spikes (Kostyuchenko et al, 2011; Mancini et al, 2000; Mukhopadhyay et al, 2006; Sherman and Weaver, 2010; Smith et al, 1995; Sun et al, 2013; Zhang et al, 2002, 2005, 2011)

Summary

Introduction

Alphaviruses are arthropod-transmitted enveloped pathogens that cause epidemics in humans and other vertebrate animals (Jose et al, 2009; Schwartz and Albert, 2010; Strauss and Strauss, 1994). Alphaviruses have an $12-kb unsegmented single-stranded (+)RNA genome that encodes four non-structural and five structural proteins (Strauss and Strauss, 1994). The icosahedral shell of alphaviruses consists of an outer layer of trans-membrane envelope E1 and E2 proteins and an inner capsid layer separated by a host-derived membrane. The capsid N-terminal domain (NTD) is disordered and binds the negatively charged alphavirus RNA genome (Owen and Kuhn, 1996)

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Results

Conclusion