The Structural Biology of Hepatitis B Virus: Form and Function

Abstract

Hepatitis B virus is one of the smallest human pathogens, encoded by a 3,200-bp genome with only four open reading frames. Yet the virus shows a remarkable diversity in structural features, often with the same proteins adopting several conformations. In part, this is the parsimony of viruses, where a minimal number of proteins perform a wide variety of functions. However, a more important theme is that weak interactions between components as well as components with multiple conformations that have similar stabilities lead to a highly dynamic system. In hepatitis B virus, this is manifested as a virion where the envelope proteins have multiple structures, the envelope-capsid interaction is irregular, and the capsid is a dynamic compartment that actively participates in metabolism of the encapsidated genome and carries regulated signals for intracellular trafficking.

Keywords: antiviral; capsid; icosahedral; nucleoprotein complex; reverse transcriptase; self-assembly.

Figure 1

A composite cryo-EM reconstruction of a dane particle. (a) Cut away views of a composite model of the HBV virion comprised of an icosahedral capsid (blue) containing packaged DNA (red) and an outer envelope (gold) with protein projections spaced 60Å apart. Views are cross-sections (left), and two cut aways (b) X-ray crystal structure of recombinant capsid (36) docked into the cryo-EM density map of the virion capsid (left). The tips of the core spikes are in close apposition but do not penetrate the envelope. Additional details and cartoon of interpretation (right). The surface protein projections are ascribed to HBsAg and are designated as large (L), medium (M), and small (S) arbitrarily. These figures reproduced with permission from Dryden et al. (29).

Figure 2

X-ray crystal structures of the assembly domain. (a) A HBcAg dimer in the context of a capsid. The helices in HBcAg are named 1–5 from N to C-terminus. The dimer interface comprises of a four-helix bundle created by two helices from each monomer. (b) a superposition of an HBcAg dimer in the context of a capsid (grey) on a free dimer (Y132A mutant) (blue). The free dimer is less compact than the dimer in the context of a capsid (c) An HBeAg dimer. The dimeric interface is drastically altered and stabilized by disulfide bonds (d) An HBcAg T=4 capsid with the asymmetric unit in color. The individual subunits are A (blue), B (red), C (green) and D (yellow) or AB and CD dimers.

Figure 3

The HBcAg CTD. (a) A schematic of the assembly domain and the CTD including the sequence of the CTD. S155, S162 and S170 are deemed to be critical for pgRNA packaging (173, 174) (b) cut-away view of a cryo-EM reconstruction of an empty Cp183 capsid. The density in color corresponds to the CTD based on the fitting of an X-ray crystal structure of a Cp149 capsid in the reconstruction. CTD density is prominent beneath the fivefold and quasi-sixfolds (c) A cryo-EM reconstruction of empty Cp183 capsids bound to SRPK molecules. SRPK (red) binds to transiently exposed CTDs at the quasi-sixfolds. These figures reproduced with permission from Selzer et al. (75) and Chen et al. (74).

Figure 4

RNA containing capsids. Icosahedral reconstructions of (a) wildtype Cp183 and (b) a phosphorylation mimic mutant with in vitro packaged pgRNA (blue and gold respectively). The pgRNA in the former forms an icosahedral cage while the same in the latter is more mesh-like (c) An asymmetric reconstruction of an RNA-containing virion shows density for pgRNA (gold), P protein (red) and other unassigned content. These figures reproduced with permission from Wang et al. (33) and Wang et al. (94).

Figure 5

HBsAg subviral particles. (a) A cryo-micrograph of a mixture of ~22nm spherical and filamentous particles. Note how some filaments vary in their diameter. The scale bars correspond to 100nm. (b) A helical real-space reconstruction of a self-consistent data set. This two-start helix has a subunit twist of 35° and rise of 9.8Å. (c) A HBcAg dimer highlighting residues that affect secretion of Dane particles but do not affect core assembly (117). Residues from different monomers are in magenta and orange, respectively. Residues that are partially obscured by interdimer interfaces are highlighted in muted colors. Panels (a) and (b) are reproduced with permission from Short et al. (110).

Figure 6

CpAMs alter the structure and dynamics of the capsid. (a) Overlays of CpAM bound capsids (magenta) on apo-capsid (cyan) when viewed down the fivefold reveal systematic differences in capsid structure in the exterior (upper panels) and interior (lower panels). This figure reproduced with permission from Venkatakrishnan et al. (b) Superpositions of Cα traces of individual dimers from CpAM bound structures (red) on the apo structures (grey).