Structural atlas of the most abundant human gut virus

Abstract Bacteriophages of the order Crassvirales (crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes and account for up to ~95% of the viral sequences in some individuals(1–4). Crassviruses are likely to play major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the phage-encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses(4,5). Here we present a cryo-electron microscopy structure of Bacteroides intestinalis bacteriophage ΦcrAss001(6), providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms a ~1 MDa assembly at the end of the tail and exhibits a previously unknown fold that we designate “crAss fold”, that likely serves as a gatekeeper to control ejection of cargoes. In addition to packing the ~103 kb virus DNA, the ΦcrAss001 virion encompasses extensive storage space for cargo proteins in the capsid and, most unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide the structural basis for understanding the mechanisms of assembly and infection of these hugely abundant crassviruses.