Fig. 1: Structure of the ΦcrAss001 virion and functional assignments.

a,b, Electron micrographs of virions recorded using negative staining (a; n = 16 micrographs) and under cryogenic conditions (b; n = 44,006 micrographs). Scale bars, 100 nm. c, Molecular surface of virion reconstruction viewed from outside (left) and z-clipped (right), coloured by gene product. DNA (grey) on the z-clipped image is depicted either as an outer layer lining the capsid wall (top left) or clipped (right), or is removed (bottom left). Unmodelled regions are displayed as map, lowpass filtered to 8 Å (parts of head fibre proteins and DNA) and to 16 Å (tail fibres, semi-transparent grey). AUX, auxiliary capsid protein; C1 and C2, cargo proteins; MUZ, muzzle protein; POR, portal protein; PVA, portal vertex auxiliary capsid protein; R1–R4, ring proteins; THA and THB, tail hub proteins. Numbers in brackets indicate the protein copy number in the virion. d, Top, the ΦcrAss001 genome (accession: NC_049977.1) region 11643–68717 showing open reading frames as arrows coloured corresponding to gene products (gp) in c, scaled according to gene length. Bottom, gene conservation, with the length of each bar representing the fraction of each crassvirus group in the order Crassvirales containing a detectable homologue, coloured corresponding to c. Names on the left refer to the virus families (Intestiviridae, Crevaviridae, Steigviridae and Suoliviridae) and groups (zeta and epsilon) with individual members from non-human gut environments represented by ProJPt-BP1 (termite gut), Fpv3 (fish farm) and Φ14:2, Φ17:2 and Φ13:2 (marine environments).