The structure of Sinorhizobium meliloti phage ΦM12, which has a novel T=19l triangulation number and is the founder of a new group of T4-superfamily phages

•The first T=19l geometry icosahedral bacteriophage structure is reported.•The T=19l geometry creates a quite large internal volume for packing the dsDNA genome.•ΦM12's capsid bows at the icosahedral faces when not packed with DNA, similar to other dsDNA phages.

ΦM12 is the first example of a T=19l geometry capsid, encapsulating the recently sequenced genome. Here, we present structures determined by cryo-EM of full and empty capsids. The structure reveals the pattern for assembly of 1140 HK97-like capsid proteins, pointing to interactions at the pseudo 3-fold symmetry axes that hold together the asymmetric unit. The particular smooth surface of the capsid, along with a lack of accessory coat proteins encoded by the genome, suggest that this interface is the primary mechanism for capsid assembly. Two-dimensional averages of the tail, including the neck and baseplate, reveal that ΦM12 has a relatively narrow neck that attaches the tail to the capsid, as well as a three-layer baseplate. When free from DNA, the icosahedral edges expand by about 5 nm, while the vertices stay at the same position, forming a similarly smooth, but bowed, T=19l icosahedral capsid.

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