How structural biology has changed our understanding of icosahedral viruses

Abstract

Cryo-electron microscopy and tomography have allowed us to unveil the remarkable structure of icosahedral viruses. However, in the past few years, the idea that these viruses must have perfectly symmetric virions, but in some cases, it might not be true. This has opened the door to challenging paradigms in structural virology and raised new questions about the biological implications of "unusual" or "defective" symmetries and structures. Also, the continual improvement of these technologies, coupled with more rigorous sample purification protocols, improvements in data processing, and the use of artificial intelligence, has allowed solving the structure of sub-viral particles in highly heterogeneous samples and finding novel symmetries or structural defects. In this review, I initially analyzed the case of the symmetry and composition of hepatitis B virus-produced spherical sub-viral particles. Then, I focused on Alphaviruses as an example of "imperfect" icosahedrons and analyzed how structural biology has changed our understanding of the Alphavirus assembly and some biological implications arising from these discoveries.

Keywords: cryo-EM; cryo-ET; icosahedral virions; virus assembly.

FIG 1

(A) The smallest icosahedron comprises 12 pentamers and 60 asymmetric subunits (red). This structure has fivefold, threefold, and twofold rotational symmetry axes and is described by a Triangulation (T) number equal to 1. This number is obtained using the formula T = h² + h * k + k², where h and k are positive integer numbers representing the shortest path from one pentamer to another; h is the number of units in the shortest straight path toward the closest pentamer, and k is the number of units that must be shifted to the right or left to go to the next pentamer. When T > 1, there are 12 pentamers, a variable, and a discrete number of hexamers. In a T = 3 icosahedron, three chemically different environments are occupied by a protein subunit (red, blue, and cyan). In contrast, in a T = 4 capsid, there are four different chemical environments (red, blue, cyan, and yellow). (B) The change in the size of an icosahedral capsid is discrete. On average, mostly T = 1, 3, and 4 capsids have a diameter of around 20, 30, and 40 nm, respectively.

FIG 2

(A) Cryo-EM map of HBVs S-HBsAg spherical SVPs from Gilbert et al. (16) shows that these SVPs have octahedral symmetry with large holes (EMD-1158). (B) The cryo-EM map of HBV from Cao et al. (31) reveals irregular spherical SVPs with no apparent symmetry (EMD-6951). (C) The cryo-EM map of Liu et al. (17) has the highest resolution for spherical HBV SVPs and results in a novel rhombicuboctahedron symmetry (EMD-26117).

FIG 3

Tomographic reconstructions of the in situ assembly intermediates of CHIKV during budding from (8). (A) The cytoplasmatic core interacts with the glycoproteins at the plasma membrane. As the budding process is completed, the virion acquires icosahedral symmetry. The highest resolution is achieved only when the particle is completely released. This suggests that the tethered particle is not completely symmetric, as the proteins are far more flexible than that in the released particle; the resolution of the reconstructions from left to right is given as 43.7, 23, 19, 13.4, and 8.2 Å. (B) The docked particle from A was rotated 90° to show the organization of the glycoproteins, forming a pentamer with a 43.8 Å resolution. (C) The sub-tomogram averages of two classes of cytosolic cores show that these particles do not have icosahedral symmetry. This figure was generated using cryo-EM maps with the accession codes EMDB-26446, EMDB-26447, EMDB-26448, EMDB-26449, EMDB-26450, EMDB-26451, and EMDB-2652.

FIG 4

Asymmetric (C₁) reconstructions of purified CHIKV particles. (A) Radially colored density maps with half-cut representation after asymmetric (C₁) reconstruction of all particles. The zooms show the well- and poorlyresolved poles. (B and C) In classes A and B, the maps exhibited a well-resolved pole opposite the poorly resolved pole. (D) In class C, the entire particle is well-resolved. The poorly resolved pole is associated with the part of the particle where pinching off the plasmatic membrane occurs. Taken with permission from (18).