The Vaccinia virion: Filling the gap between atomic and ultrastructure

Abstract

We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking, identifying 4609 unique-mass crosslink ions at an effective FDR of 0.33%, covering 2534 unique pairs of crosslinked protein positions, 625 of which were inter-protein. The data were statistically non-random and rational in the context of known structures, and showed biological rationality. Crosslink density strongly tracked the individual proteolytic maturation products of p4a and p4b, the two major virion structural proteins, and supported the prediction of transmembrane domains within membrane proteins. A clear sub-network of four virion structural proteins provided structural insights into the virion core wall, and proteins VP8 and A12 formed a strongly-detected crosslinked pair with an apparent structural role. A strongly-detected sub-network of membrane proteins A17, H3, A27 and A26 represented an apparent interface of the early-forming virion envelope with structures added later during virion morphogenesis. Protein H3 seemed to be the central hub not only for this sub-network but also for an ‘attachment protein’ sub-network comprising membrane proteins H3, ATI, CAHH(D8), A26, A27 and G9. Crosslinking data lent support to a number of known interactions and interactions within known complexes. Evidence is provided for the membrane targeting of genome telomeres. In covering several orders of magnitude in protein abundance, this study may have come close to the bottom of the protein-protein crosslinkome of an intact organism, namely a complex animal virus.

Spatial, Quantitative and Functional Deconstruction of Virus and Host Protein Interactions Inside Intact Cytomegalovirus Particles

“…A protein-protein interaction network of the intact HCMV particle XL-MS allows capturing protein contacts from native environments 15 such as organelles [16][17][18][19][20] . We reasoned that XL-MS is also suitable for gaining global insights into PPI networks of large and structurally heterogeneous herpesviral particles.…”

Loss of the Vaccinia Virus 35-Amino-Acid Hydrophobic O3 Protein Is Partially Compensated by Mutations in the Transmembrane Domains of Other Entry Proteins

“…Since D8 is a cell attachment protein (24), it may have an ancillary effect. However, a more direct effect is not excluded, as chemical cross-linking provided evidence for the close proximity of D8 and the A21 EFC protein (13).…”

“…However, they lack signal peptides and are nonglycosylated, raising questions regarding their mode of trafficking to the viral membrane. The structure of the EFC has not yet been determined, though some subunit interactions have been identified (10)(11)(12)(13) and the crystal structures of the ectodomains of two have been reported (14,15).…”

Vaccinia viral A26 protein is a fusion suppressor of mature virus and triggers membrane fusion through conformational change at low pH

“…activation of viral membrane fusion by “de-repression” of a viral fusion suppressor. In the report by Gershon et al, the N-terminal region of A26 was proposed to interact with the N-terminal of G9 and the C-terminal of ATI based on crosslinking analysis [54]. However, the protein structures of G9, A16 and ATI remain unresolved.…”