Hepatitis A Virus Capsid Structure

Abstract

Hepatitis A virus (HAV) has been enigmatic, evading detailed structural analysis for many years. Its recently determined high-resolution structure revealed an angular surface without the indentations often characteristic of receptor-binding sites. The viral protein 1 (VP1) β-barrel shows no sign of a pocket factor and the amino terminus of VP2 displays a "domain swap" across the pentamer interface, as in a subset of mammalian picornaviruses and insect picorna-like viruses. Structure-based phylogeny confirms this placement. These differences suggest an uncoating mechanism distinct from that of enteroviruses. An empty capsid structure reveals internal differences in VP0 and the VP1 amino terminus connected with particle maturation. An HAV/Fab complex structure, in which the antigen-binding fragment (Fab) appears to act as a receptor-mimic, clarifies some historical epitope mapping data, but some remain difficult to reconcile. We still have little idea of the structural features of enveloped HAV particles.

Figure 1.

HAV structural proteins and their topography. (A) Schematic of polypeptide intermediate 1 (P1) genome organization. The numbers of amino acids in the polypeptides are shown. The color scheme is viral protein 1 (VP1), blue; VP2, green; VP3, red; VP4, yellow; this is used throughout the figures. (B) Surface overview: the hepatitis A virus (HAV) accessible surface. White lines clarify the particle facets.

Figure 2.

Distinctive structural features of hepatitis A virus (HAV). (A) No canyon depression. Side view of surface of protomer of HAV (gray) overlaid on a ribbon depiction of an enterovirus 71 (EV71) protomer with the proteins color-coded as in Figure 1B. This highlights the loops, which are labeled, that are truncated in HAV to flatten out the canyon. (B) Potential glycophorin A receptor-binding site. A pentamer from the HAV capsid with viral protein (VP)1–3 drawn in cartoon representation showing the location of residues implicated in the glycophorin A receptor-binding site as spheres: magenta VP1 Lys 221 and gray 102–221 VP3. (C) VP1 extensions. Side-by-side surface renditions of an HAV pentamer (left) and a Ljungan virus (LV) pentamer (right). The magenta spheres highlight the last VP1 residue visible in HAV beyond which are ∼3 VP1 residues and the 2A extension that would be present in the enveloped particle. On the LV pentamer, the residues corresponding to the extended VP1 carboxy-terminus are drawn in royal blue. (D) Lack of hydrophobic pocket in VP1 β-barrel compared with an enterovirus. An HAV protomer (left) is drawn in cartoon representation alongside that for EV71 (right). The pocket volume calculated with PyMOL is drawn in light blue mesh. The lipid that binds in the EV71 pocket is drawn in magenta sticks.

Figure 3.

Structural features. (A) Viral protein (VP)2 domain swap. A surface-rendered protomer of hepatitis A virus (HAV) is depicted with the VP2 amino terminus differentiated by being drawn in green cartoon representation. The VP2 amino termini from Ljungan virus (LV) and foot-and-mouth disease virus (FMDV) are superimposed and depicted in cyan and magenta, respectively. It can be seen that both LV and HAV share the domain swap conformation characteristic of insect picorna-like viruses rather than the classical picornavirus conformation represented by FMDV. (B) Structure-based phylogenetic tree of representative picornaviruses and cripaviruses. Included in the analysis are 3VBF (EV71), 1BEV (bovine enterovirus), 4HRV (human rhinovirus14), 1EAH (poliovirus type2), 1COV (coxsackievirus B3), 1TME (Theiler’s virus), 3MEV (mengo virus), 3CJI (Seneca Valley virus), 1ZBA (FMDV A10), 2WFF (equine rhinitis A virus [ERAV]), 3NAP (triatoma virus [TrV]), 5GKA (aichi virus), 3JB4 (LV), and 1B35 (cricket paralysis virus [CrPV]). Evolutionary distance is calculated based on the number of unmatched residues and the deviation among matched residues. Residues corresponding to the HAV VP2 switch region (1–53) are excluded although their inclusion does not affect the result. (C) Disordered region in the empty particle. HAV is viewed from the inside with blue mesh corresponding to positive |F_o-F_c| electron density calculated taking the correctly positioned empty HAV from the full HAV. This shows that VP1 2–28 and VP2 5–17 around the threefold axis are better defined in the full particle.

Figure 4.

Location of endosomal sorting complex required for transport (ESCRT) late-domain motifs. Late-domain YPX₃L motifs are shown as magenta spheres on the pentamer of hepatitis A virus (as drawn in Fig. 2A). In the inset box, a close-up of the residues that are accessible is shown in the context of the accessible surface.

Figure 5.

R10 antibody interactions with hepatitis A virus (HAV). (A) Surface of the cryoelectron microscopy (cryo-EM) complex for R10 and HAV based on the 4.2 Å resolution cryo-EM structure of the R10 antigen-binding fragment (Fab)/HAV full particle complex. The virus surface is color-coded blue to red according to distance from the particle center while the Fab molecules are shown in red. One icosahedral asymmetric unit is indicated by a white triangle. (B) Surface maps of HAV generated using radial interpretation of viral electron density maps (RIVEM) (Chapman and Rossmann 1993). Residues of VP1, VP2, and VP3 are shaded in pale blue, green, and red, respectively; residues involved in binding to R10 are shown in brighter colors corresponding to the protein chain they belong to, and are outlined by blue and yellow lines. An icosahedral protomer is outlined in purple with the symmetry axes labeled. (From Wang et al. 2017; panel reproduced (A) and modified (B), respectively, with permission from the author.)