Refinement of the full particle structure stuck at an R-factor of 31

Refinement of the full particle structure stuck at an R-factor of 31.8%, probably attributable to imperfect isomorphism of the constituent crystals and to the extreme weakness of the data. to receptor binding sites. Peptide scanning AF-9 data extends the previously reported VP3 antigenic site4, while structure-based predictions5 suggest further epitopes. HAV contains no pocket factor, can withstand remarkably high temperature and low pH, with vacant particles being even more strong than full particles. The computer virus probably uncoats via a novel mechanism, being built differently to other picornaviruses. It utilizes a VP2 domain name swap characteristic of insect picorna-like viruses6,7 and structure-based phylogenetic analysis places HAV between common picornaviruses and the insect viruses. The enigmatic properties of HAV may reflect its position as a link between modern picornaviruses and the more primitive precursor insect viruses, for instance HAV retains the ability to move from cell-to-cell by transcytosis8,9. HAV is unique amongst picornaviruses in targeting the liver and continues to be a source of mortality despite a successful vaccine10. HAV isolates belong to a single serotype11. Unlike other picornaviruses HAV cannot shut down host protein synthesis, has a highly MPTP hydrochloride deoptimized codon usage and grows poorly in tissue culture. Particles are produced with a 67 residue C-terminal extension of VP1, which is usually implicated in particle assembly (this longer form of VP1 is known as VP1-2A or PX)12. Particles containing the extension shroud themselves in host membrane to create enveloped viruses2. The extension is usually cleaved by host proteases to yield mature capsids12. Whilst picornavirus VP4 is generally myristoylated this does not happen in HAV13, indeed the putative VP4 is very small (~23 residues13) and it has remained unclear if it is present in computer virus particles14. The cell surface molecule T cell Ig and mucin 1 (TIM-1)15 acts as a receptor for HAV, and although transcytosis occurs8,9 it is not clear how the computer virus gets to the liver, its principal site of replication. We have analysed formaldehyde inactivated HAV genotype TZ84 (Methods). Two types of particles were separated, one made up of significant amounts of viral RNA (Extended Data Fig. 1). In the RNA-containing full particles VP0 is at least partially cleaved and we detect VP4, as for other picornaviruses, whilst the vacant particles harbour only VP0, and are probably similar to the MPTP hydrochloride vacant particles frequently seen in picornavirus infections (Methods and Extended Data Fig. 1). It remains unclear whether such vacant particles can encapsidate RNA and lie on the route to assembly of full particles. Even full particles appear to contain more uncleaved VP0 than is seen in MPTP hydrochloride other picornaviruses, in-line with observations that VP0 cleavage is usually protracted16. The sedimentation coefficients are 144S and 82S for the full and vacant particles respectively (Extended Data Fig. 1). 144S is usually a little less than the 155S expected for a full enterovirus particle while the vacant particle has a comparable S-value to that observed for the more expanded vacant enterovirus particles17. Very thin crystals (~1001005 m3) were obtained for both particles. Diffraction data were collected at Diamond beamlines I03 and I24. Data were collected at 100K to avoid beam induced crystal movement at room heat (Supplementary Video 1), and were used to produced reliable atomic models at 3.0 and 3.5 ? resolution for the full and vacant particles respectively (Methods and Extended Data Table 1). The external surface of HAV is usually smooth, with no canyon (Fig. 1a)18; shortening of the VP1 BC loop lowers the north wall while reductions in the VP2 EF and VP1 GH loops ablate the south wall of the canyon (Fig. 1b). Compared to foot-and-mouth-disease computer virus, the loops at the 5-fold and 3-fold axes in HAV are slightly raised, giving the computer virus the appearance of a facetted triakis icosahedron (Fig. 1a). In-line with the low buoyant density in CsCl19 there are no apertures in the capsid to permit the entry of Cs+ ions. The major capsid proteins, VP1-3 MPTP hydrochloride comprise eight-stranded anti-parallel -barrels, follow the expected pseudo T=3 arrangement and span the thickness of the capsid (Extended Data Fig..