Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy

Abstract

The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.

Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure

“…There are minimal conformational differences throughout the rest of the Johnson fold. This is different than observed in other Caudoviruses such as phage Sf6, where there is conformational variability throughout the Johnson fold (Zhao et al, 2017).…”

“…The interaction area between two adjacent MCP proteins is ~3150 Å 2 , which is larger than most other T=7 Johnson folds. Only phage Sf6 buries more surface area (~3277 Å 2 ), much of which is contributed by the large insertion domain that makes intracapsomer interactions (Zhao et al, 2017). (We note that phage Sf6 lacks a decoration protein.…”

Flexible Connectors between Capsomer Subunits that Regulate Capsid Assembly

“…E-loop-like structural elements occur in many capsids which range in size from T=1 to T=16 and include the well-studied bacteriophages P22 [28–30], T4 [31], T5 [32], T7 [33], as well as epsilon15 [34], BPP-1 [35], Sf6 [36], three bacterial encapsulins [37–39], Herpesvirus nucleocapsids [40] and have been inferred in many others, including ϕ29[41] and P2[42]. While the E-loop was first revealed as a structural element involved in forming the covalent bonds that stabilize the HK97 capsid [16], none of the examples above use such covalent crosslinks, so crosslinking is probably only a minor, late-acquired role for the E-loop.…”

Atomic cryo-EM structures of viruses

“…It took significant effort over a long period of time [23] to achieve 3.44 Å resolution crystal structure of the ~650 Å diameter bacteriophage HK97 VLP [24,25]. In contrast, a single cryo-EM session was used recently to reach a 2.9 Å resolution structure of the icosahedral capsid of bacteriophage Sf6 virion of similar size (Figure 1D) [26**]. This, together with other near atomic resolution cryo-EM structures of large bacterial viruses [27,28,29], has led to new and unbiased understanding enabled by more reliable atomic models.…”

“…more subunits of the same protein localized at quasi-equivalent environments in an asymmetric unit [47]. Although the conformations of these subunits can vary significantly, for example, the subunits in the “T=2” inner shell of dsRNA viruses [10,48] and the T=7 dsDNA phages [9,25,26**,27,28], the conformations of these subunits in many viruses, for example, rotavirus VP6 trimers [7,14*], are indistinguishable even at near-atomic resolutions. NCS averaging of these subunits can effectively increase the total symmetry of the particles up to 60T and significantly reduce the number of particles required to reach high resolutions.…”