Cryo-EM of a Divergent Herpesvirus Reveals Structural Conservation and Novelty Including a Portal-Vertex Tegument Protein with Multiple Macrodomain-like Folds

Abstract

Ictalurid herpesvirus 1 (channel catfish virus) is an evolutionarily distant relative of human herpesviruses, from which it is thought to have diverged >400M years ago. Using cryogenic electron microscopy (cryo-EM) combined with symmetry-breaking and particle subtraction approaches, we determined structures of both the immature capsid and virion of IcHV-1. Due to limited genome annotation, we used the machine learning-based tool ModelAngelo for de novo model building, enabling unambiguous protein identification even at marginal resolutions. Notably, the IcHV-1 virion was found to have a substantial and elaborate portal-vertex associated tegument (PVAT) complex. Overall, we determined the identities and structures of ten IcHV-1 proteins: the major capsid protein; the triplex proteins; two novel virion-associated inner tegument proteins; the portal protein; and a further four PVAT proteins. Our findings reveal a high degree of fold conservation in the core capsid proteins when compared with those of human herpesviruses, but also considerable structural novelty, including for the first time in a herpesvirus, identification of a protein that has four putative macrodomains.