Structures of pseudorabies virus capsids

Abstract

Pseudorabies virus (PRV) is a major etiological agent of swine infectious diseases and is responsible for significant economic losses in the swine industry. Recent data points to human viral encephalitis caused by PRV infection, suggesting that PRV may be able to overcome the species barrier to infect humans. To date, there is no available therapeutic for PRV infection. Here, we report the near-atomic structures of the PRV A-capsid and C-capsid, and illustrate the interaction that occurs between these subunits. We show that the C-capsid portal complex is decorated with capsid-associated tegument complexes. The PRV capsid structure is highly reminiscent of other α-herpesviruses, with some additional structural features of β- and γ-herpesviruses. These results illustrate the structure of the PRV capsid and elucidate the underlying assembly mechanism at the molecular level. This knowledge may be useful for the development of oncolytic agents or specific therapeutics against this arm of the herpesvirus family.

Fig. 1. Icosahedral and sub-particle reconstructions of PRV C- and A-capsids.

a, b Shaded-surface representations of the PRV C-capsid (a) and A-capsid (b) revealing the presence of capsid-associated tegument complexes (CATCs) on the C-capsid. c–e Reconstructions for sub-particles extracted for the 5-fold (c), 3-fold (d), and 2-fold (e) of the C-capsid, respectively. f–h Reconstructions for sub-particles extracted for the 5-fold (f), 3-fold (g), and 2-fold (h) of the A-capsid, respectively.

Fig. 2. Atomic models of the PRV C- and A-capsids.

a Density map of an icosahedral asymmetric unit of the C-capsid, segmented from the three main-axis sub-particle reconstructions and colored by protein type: MCP (gray), Tri1 (red), Tri2A (blue), Tri2B (green), SCP (orange-red), and CATC (cyan). Representative superimposed atomic models of protein subunits from C-capsid (rainbow-colored from blue to red) and A-capsid (gray) are shown next to the density map as ribbons. b A schematic representation of above asymmetric unit (shaded) of the capsid. c Segmented density maps (mesh) and corresponding atomic models of MCP which illustrate side chain features. Residues with side chains are labeled. Abbreviations: CATC Capsid-associated tegument complexes; MCP Major capsid protein; SCP Small capsid protein; Tri Triplex.

Fig. 3. MCP structure and MCP-MCP interactions.

a Canonical hexon MCP (C5 hexon MCP) that colored and labeled by domain. b Superposition of the hexon and penton MCPs. c Pipe-and-plank depiction of an E-hexon and a penton showing the central channel (dashed circular). The narrowest regions of the hexon (top) and penton (below) have a dimension of about 11–13 Å. d Part of the MCP network viewed from outside (left) and inside (right). e Interactions between hexon and penton MCPs. f, g Interactions between hexon MCPs (type I, II, and III interactions; see main text). Abbreviation, MCP Major capsid protein.

Fig. 4. Structure of the triplex and characterization of the Tri1 N-terminus.

a Inside-out view of the density map of triplex Tb with surrounding MCPs. b–d Atomic model of Tb (b) and its components Tri2A and Tri2B (c, d). Superposition of Tri2A and Tri2B shows consistency in their trunk domains and conformational differences in their embracing arm domains (c). e, f Density maps of triplex Tb (e) and Tc (f) shows distinctions in the under-floor densities (colored in gray). g A close-up view of the density map (gray mesh) of the Tri1 N-terminal region with the fitted atomic model (ribbon/sticks) shown in the dashed box. h Comparison of the under-floor densities of Tbs from different herpesviruses. Abbreviations: MCP Major capsid protein.

Fig. 5. Structure of SCPs and interactions with MCPs.

a Atomic model of an SCP monomer shown as ribbons, rainbow-colored from the N-terminus (blue) to the C-terminus (red), with (up) and without (low) the corresponding density map (gray surface). b Crosslinking of six SCP subunits to form a gear-shaped hexameric ring crowning the C hexon. c SCP bridging two underlying MCPs (MCP C4 and C5). The hairpin loop of SCP C4 inserts into a groove formed by MCP C5 and SCP C5. d Open-book view of the electrostatic potential surfaces of SCP C4 and MCP C4 showing complementary electrostatic surface charges. Abbreviations: MCP Major capsid protein; SCP Small capsid protein.

Fig. 6. Architecture of the PRV C-capsid with portal and CATCs.

a The unsharpened C5 reconstructed maps of the PRV C-capsid is presented showing a cropped view of the interior density. b, c Clipped (b) and zoomed-in (c) views of the C5 capsid reconstruction showing packaged double-stranded (ds)DNA within the capsid (b) and structural components around the portal vertex (c). d, e Sub-particle reconstructions of the penton vertex (d) and the portal vertex (e). f Rotated view of (c) with a fitted model of the C5 portal protein (helix bundle) and the C12 portal protein. This view shows the interactions between the portal proteins and CATCs and triplexes beneath. g Segmented density map of the CATCs and the corresponding model. h Penton vertex sub-particle reconstruction. The CATC helix bundle is near two densities (orange circles), which are likely the head domains of capsid vertex component 2 (CVC2)-A and CVC2-B. i Portal vertex reconstruction. The CATC helix bundle is connected to the portal cap (cyan circle). j, k Comparisons of maps (j) and corresponding models (k) of CATCs from the penton and portal vertices. There is a counterclockwise (6°) rotation of the CATCs when bound to the portal vertex. l Comparison of triplexes: Ta in external orientation relative to Tc in the penton and portal vertexes. Ta in the penton vertex rotates 120° counterclockwise around its apical domain. Abbreviations: CATC Capsid-associated tegument complex; MCP Major capsid protein; SCP Small capsid protein; Tri Triplex.