Breaking the symmetry of a viral capsid.

The small size, and thus coding capacity, of viral genomes necessitates the repetitive use of identical building blocks in constructing the viral capsid. This genetic economy gives rise to highly symmetric structures, typically with either helical or icosahedral geometries. Assembly of symmetric viral capsids is believed to proceed via “conformational switching” of individual protein subunits (1–3). In this model, a special nucleation event initiates the assembly process, and in subsequent assembly steps, each protein that binds to the growing structure undergoes a conformational change that creates a new binding site for the next protein to assemble. Although the use of icosahedral symmetry in capsid assembly provides an elegant solution to the need for genetic economy, assuming the entire capsid obeys this symmetry is an oversimplification that does not adequately reflect the complexity of biology (4, 5). Indeed, the viral genome itself is present as only a single copy and thus cannot assume the icosahedral symmetry of the surrounding capsid. Additionally, it is imperative that regions of the virus shell deviate from the global icosahedral symmetry of the capsid to successfully accomplish critical aspects of the viral life cycle such as genome packaging/release and host cell recognition/attachment (4, 6–9). Until recently, structural biology has largely ignored these essential deviations from symmetry. For technical reasons, X-ray and cryo-electron microscopy (cryo-EM) structures of viruses typically impose icosahedral symmetry and are thus incapable of illuminating the subtle structural rearrangements of the capsid necessary to successfully navigate the viral life cycle. In PNAS, Gorzelnik et al. (10) present an asymmetric cryo-EM reconstruction of the bacterial virus Qβ that provides insights into the assembly pathway of the virus, the organization of the genetic material within the viral capsid, and the potential coupling of host cell recognition and genome release. Bacteriophage Qβ belongs to the Leviviridae family of small, positive-sense, single-stranded RNA bacteriophages (11) (Fig. 1 A and B). These viruses infect their Gram-negative bacterial hosts via adsorption to bacterial pili. The Leviviridae have small, ∼4-kb, genomes that encode amaturation protein, the capsid protein, and a subunit of an RNA-dependent RNA replicase (12, 13). MS2-like Leviviridae phages encode an additional lysis protein, whereas in the Qβ-like phages, lysis is carried out by the maturation protein Fig. 1. Schematic of a typical Leviviridae virus and the X-ray crystallographic structure of bacteriophage Qβ. (A) Schematic of the T = 3 capsid of a typical Leviviridae virus. Three quasiequivalent subunits are colored red, green, and blue, respectively. (B) Schematic cross-section of a typical Leviviridae virus showing the encapsidated single-stranded positive-sense RNA genome. The capsid protein, maturation protein, and RNA genome are labeled. (C) Ribbon diagram of the X-ray crystallographic structure of the T= 3 bacteriophageQβ capsid (12) [Protein Data Bank (PDB) ID code 1QBE]. Quasiequivalent subunits in the T = 3 icosahedral lattice are colored red, green, and blue, respectively. The icosahedral asymmetric unit is shown as a black triangle with the positions of twofold, threefold, and fivefold symmetry axes indicated. (D) Crystallographic asymmetric unit of the bacteriophage Qβ X-ray crystal structure (12) (PDB ID code 1QBE). Ribbon diagrams in C and D were rendered using CHIMERA (21).