High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

Abstract

Sf6 is a bacterial virus that infects the human pathogen Shigella flexneri. Here, we describe the cryo–electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae.

Journey to the center of the phage; revealing the ejectosome of Pectobacterium bacteriophage ΦM1

“…S4AB). A similar phenomenon was previously described in which the portal of podophage SF6 exists in two discrete populations, separated by a 6° rotation about the Z axis (35). In our 3D classifications, we also identified two populations of particles in which ejectosome structures were aligned, but portal density was also rotated by ~6° about the Z axis This suggests that the ΦM1 portal may also exist as two discrete particle populations (Fig.…”

Structural Study of the Cobetia marina Bacteriophage 1 (Carin-1) by Cryo-EM

“…Overall, our results are, to our knowledge, the first high resolution structures of a complete marine bacteriophage, the fourth full mature structure of a Gram-negative infecting podovirus and the second T7-like podovirus structure (9,12,24,25,35). This structure is showing great structure similarity with known podophages despite the low sequence homology.…”

Cryo-EM analysis of Pseudomonas phage Pa193 structural components

“…1c) and lacks density for the rst 93 amino acids. These residues were not identi ed by LC-MS and may be cleaved during maturation or are invisible in the reconstruction due to the symmetry mismatch between portal and capsid proteins 32 .…”