Cryogenic electron microscopy and tomography reveal imperfect icosahedral symmetry in alphaviruses.
David Chmielewski, Guan-Chin Su, Jason T Kaelber, Grigore D Pintilie, Muyuan Chen, Jing Jin, Albert J Auguste, Wah Chiu
Author Information
David Chmielewski: Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA. ORCID
Guan-Chin Su: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. ORCID
Jason T Kaelber: Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. ORCID
Grigore D Pintilie: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. ORCID
Muyuan Chen: Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
Jing Jin: Vitalant Research Institute, San Francisco, CA 94118, USA.
Albert J Auguste: Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. ORCID
Wah Chiu: Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA. ORCID
Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) reconstructions, which impose icosahedral symmetry on the viral particles. Using cryogenic electron tomography (cryo-ET), we revealed a polarized symmetry defect in the icosahedral lattice of Chikungunya virus (CHIKV) in situ, similar to the late budding particles, suggesting the inherent imperfect symmetry originates from the final pinch-off of assembled virions. We further demonstrated this imperfect symmetry is also present in in vitro purified CHIKV and Mayaro virus, another arthritogenic alphavirus. We employed a subparticle-based single-particle analysis protocol to circumvent the icosahedral imperfection and boosted the resolution of the structure of the CHIKV to ∼3 Å resolution, which revealed detailed molecular interactions between glycoprotein E1-E2 heterodimers in the transmembrane region and multiple lipid-like pocket factors located in a highly conserved hydrophobic pocket. This complementary use of in situ cryo-ET and single-particle cryo-EM approaches provides a more precise structural description of near-icosahedral viruses and valuable insights to guide the development of structure-based antiviral therapies against alphaviruses.
