Architecture of the flexible tail tube of bacteriophage SPP1

Maximilian Zinke,Sophie Zinn-Justin,Katrin A A Sachowsky,Gunnar F Schröder,Carl Öster,Michael Habeck,Adam Lange,Raimond Ravelli

doi:10.1038/s41467-020-19611-1

Abstract

Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.

Highlights

Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis
Structural information was limited to pseudo-atomic models, which were generated for SPP16 based on solution nuclear magnetic resonance (NMR)
The use of an exact symmetry is justified by the NMR data that are only consistent with a highly symmetric sample

Summary

Results

4D and 3D proton-detected ssNMR experiments at 40 kHz magic-angle spinning (MAS) and 900 MHz proton Larmor frequency were used to probe long-range distance restraints between the following: 1) amide groups (Fig. 1c, left panel)38,39; 2) methyl groups; 3) methyl and amide groups globally (Fig. 1c, right panel); 4) methyl and amide groups at protein-protein interfaces All of these experiments generated highly unambiguous restraints due to their highdimensionality (4D) or spectral simplicity (amino-acid specific methyl labeling)—as visualized in Fig. 1d where a set of consistent restraints (amide-amide and methyl-amide contacts) defines the inner β-barrel motif of the tail tube formed by the β-strands β2.2, β3.2, β6.1, and β5.2.

14 Met-methyl

Methods

30 Gly 39

Code availability