Crystal structure of Swine vesicular disease virus and implications for host adaptation

Abstract

Swine vesicular disease virus (SVDV) is an Enterovirus of the family Picornaviridae that causes symptoms indistinguishable from those of foot-and-mouth disease virus. Phylogenetic studies suggest that it is a recently evolved genetic sublineage of the important human pathogen coxsackievirus B5 (CBV5), and in agreement with this, it has been shown to utilize the coxsackie and adenovirus receptor (CAR) for cell entry. The 3.0-A crystal structure of strain UK/27/72 SVDV (highly virulent) reveals the expected similarity in core structure to those of other picornaviruses, showing most similarity to the closest available structure to CBV5, that of coxsackievirus B3 (CBV3). Features that help to cement together and rigidify the protein subunits are extended in this virus, perhaps explaining its extreme tolerance of environmental factors. Using the large number of capsid sequences available for both SVDV and CBV5, we have mapped the amino acid substitutions that may have occurred during the supposed adaptation of SVDV to a new host onto the structure of SVDV and a model of the SVDV/CAR complex generated by reference to the cryo-electron microscopy-visualized complex of CBV3 and CAR. The changes fall into three clusters as follows: one lines the fivefold pore, a second maps to the CAR-binding site and partially overlaps the site for decay accelerating factor (DAF) to bind to echovirus 7 (ECHO7), and the third lies close to the fivefold axis, where the low-density lipoprotein receptor binds to the minor group of rhinoviruses. Later changes in SVDV (post-1971) map to the first two clusters and may, by optimizing recognition of a pig CAR and/or DAF homologue, have improved the adaptation of the virus to pigs.

FIG. 1.

Sample region of an Fo-Fc omit map (omitting residues 130 to 137 of VP1). The electron density is shown as a blue mesh. SVDV residues and CAV9 residues from the same loop are shown as red and yellow ball-and-stick diagrams, respectively, and are labeled in the corresponding colors. The electron density clearly shows that the SVDV phases have no residual bias from the CAV9 model used to produce them. Figures were generated with a version of MOLSCRIPT (36) modified by R. Esnouf (11, 12) and with Raster3D (46).

FIG.2.

Structure of SVDV. (A) Depicted centrally is an SVDV capsid comprising 60 copies of the proteins VP1, -2, -3, and -4. The proteins are shown as “worms” and are color coded (VP1 is blue, VP2 is green, VP3 is red, and VP4 is yellow). A protomeric unit (one copy each of VP1 to -4) is omitted. Around the periphery of the capsid a copy of each of the SVDV proteins is shown as a worm in red. Superimposed on each is a copy of the similar protein from CBV3 (green), CAV9 (yellow), and PV type 3 (blue). The pocket factor is depicted in aquamarine within the VP1 β-barrel. (B) Chain traces of SVDV (red) superimposed on CBV3 (green) around a fivefold vertex. Myristoyl groups are shown as ball-and-stick representations and colored green or red, respectively. Residue Arg 132 is shown as a blue ball-and-stick representation. The ions on the fivefold axis are shown in lilac.

FIG. 3.

Structure-based alignment (61) of the SVDV capsid proteins with those of CBV3 and CAV9. Conserved residues are shown boxed with a black background. Helices and strands assigned by definition of secondary structure of proteins (DSSP) (31) are labeled corresponding to standard picornaviral nomenclature and are represented by coils and arrows, respectively. Solvent accessibility (acc) within a pentamer was calculated by DSSP and is shown by the graduations in the bar below the sequence. Black graduations, relative accessibility of >40%; gray graduations, relative accessibility of >10%. This figure was produced using Espript (20).

FIG. 4.

Ligplot (63) representations of the VP1 hydrophobic pockets of SVDV and CBV3.

FIG. 5.

Sequence variation and receptor binding. (Top) Orthogonal views of an SVDV pentamer are shown with the proteins shown as worms in gray. Amino acid substitutions between CBV5 and SVDV are shown in green and substitutions that have occurred in SVDV since 1971 are depicted in orange. Residues in cluster 2 also correspond to the site of DAF binding in ECHO7 (25). (Bottom) Orthogonal views of an SVDV/CAR complex modeled based on the CBV3/CAR complex coordinates (PDB code 1JEW) (6). The CAR receptor is shown in aquamarine.