Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus

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Abstract
Structural determinations of spherical viruses have so far been limited to the capsid shell with icosahedral symmetry. Now for the first time an entire spherical virus structure has been determined without imposing icosahedral symmetry, a strategy that was necessary to simplify image reconstruction calculations. The virus in question is epsilon15 phage, which infects the human pathogen Salmonella anatum so is a potential therapeutic agent for salmonellosis. Single-particle cryo-electron microscopy shows the icosahedral protein shell to consist of 60 hexamers and 11 pentamers. Non-icosahedral components cluster at one of the twelve capsid vertices, through which DNA is packaged and released. The genome is packed in coaxial coils and a previously unidentified protein core wraps around the terminal end of the DNA. The shell resembles those of other dsDNA viruses including herpesvirus, suggesting a common ancestor. The critical viral components for packaging DNA, recognizing and binding to host cells, and injecting the condensed DNA into the host are organized at a single vertex of many icosahedral viruses. These component structures do not share icosahedral symmetry and cannot be resolved using a conventional icosahedral averaging method. Here we report the structure of the entire infectious Salmonella bacteriophage epsilon15 (ref. 1) determined from single-particle cryo-electron microscopy, without icosahedral averaging. This structure displays not only the icosahedral shell of 60 hexamers and 11 pentamers, but also the non-icosahedral components at one pentameric vertex. The densities at this vertex can be identified as the 12-subunit portal complex sandwiched between an internal cylindrical core and an external tail hub connecting to six projecting trimeric tailspikes. The viral genome is packed as coaxial coils in at least three outer layers with ∼90 terminal nucleotides extending through the protein core and the portal complex and poised for injection. The shell protein from icosahedral reconstruction at higher resolution exhibits a similar fold to that of other double-stranded DNA viruses including herpesvirus2,3,4,5,6, suggesting a common ancestor among these diverse viruses. The image reconstruction approach should be applicable to studying other biological nanomachines with components of mixed symmetries.