Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding

Abstract

Hepatitis E virus (HEV), a small, non-enveloped RNA virus in the family Hepeviridae, is associated with endemic and epidemic acute viral hepatitis in developing countries. Our 3.5-A structure of a HEV-like particle (VLP) shows that each capsid protein contains 3 linear domains that form distinct structural elements: S, the continuous capsid; P1, 3-fold protrusions; and P2, 2-fold spikes. The S domain adopts a jelly-roll fold commonly observed in small RNA viruses. The P1 and P2 domains both adopt beta-barrel folds. Each domain possesses a potential polysaccharide-binding site that may function in cell-receptor binding. Sugar binding to P1 at the capsid protein interface may lead to capsid disassembly and cell entry. Structural modeling indicates that native T = 3 capsid contains flat dimers, with less curvature than those of T = 1 VLP. Our findings significantly advance the understanding of HEV molecular biology and have application to the development of vaccines and antiviral medications.

Fig. 1.

Structure of the hepatitis E virus-like particle (VLP) (T = 1). (A) Crystal structure of HEV VLP. The 3 domains, S, P1, and P2 are colored blue, yellow, and red, respectively. The VLP is positioned in a standard orientation with the 3 2-fold icosahedral symmetry axes aligned along the vertical, horizontal, and viewing directions, respectively. (B) Cryo-EM reconstruction at 14 Å resolution. The surface is colored by radial depth cue from blue, yellow, to red. (C) HEV VLP with only the S domain. (D) VLP with S and P1 domains. (E) VLP with P1 and P2 domains.

Fig. 2.

The structure of HEV-CP. (A) One HEV-CP molecule. The molecule is rainbow colored with the N terminus in blue and the C terminus in red. (B) Secondary structure assignment. α-helices are shown by tubes, β-strands by arrows, loops by thick lines, and disordered regions by dotted lines. Regions from the S, P1, and P2 domains are colored in blue, yellow, and red, respectively, as in Fig. 1. The conventional naming scheme for the 8 β-strands (BIDG and CHEF) from the jelly-roll β-barrel is shown in parentheses. (C) P1 domain and endosialidase β-barrel domain. The sialic acid molecule is shown by sticks. Compared to (A), the P1 domain is rotated along the vertical axis by approximately 90° [viewed from left in A] to get a better view of the sialic acid binding site. (D) P2 domain and norovirus receptor binding domain. The blood-group polysaccharide is shown by sticks. The P2 domain has also been rotated compared to (A) to get a better view of the polysaccharide binding site. Secondary structural elements in P1 and P2 for putative sugar binding are highlighted by asterisks.

Fig. 3.

HEV VLP capsomeres. (A and B) HEV-CP pentamer. A reference molecule is colored according to domain organization with S in red, P1 in yellow, and P2 in red. Other molecules are shown with a single color only. (C and D) HEV-CP trimer. (E and F) HEV-CP dimer. (A, C, and E) are viewed from the side, whereas (B, D, and F) are viewed along the symmetry axes from the outside of the VLP.

Fig. 4.

T = 3 HEV capsid model. (A) The overall structure. The 3 quasi-equivalent CP molecules A–C are colored blue, red, and yellow, respectively. One asymmetric unit is highlighted along with icosahedral symmetry axes. (B) T = 1 VLP dimer. (C) T = 3 A-B dimer. (D) T = 3 C-C dimer. All 3 dimers are viewed from the side of their 2-fold symmetry axes. The line drawings at the bottom of the CP dimers illustrate the different hinge angles observed in different dimers.