Twenty-Five Years of Structural Parvovirology

Abstract

Parvoviruses, infecting vertebrates and invertebrates, are a family of single-stranded DNA viruses with small, non-enveloped capsids with T = 1 icosahedral symmetry. A quarter of a century after the first parvovirus capsid structure was published, approximately 100 additional structures have been analyzed. This first structure was that of Canine Parvovirus, and it initiated the practice of structure-to-function correlation for the family. Despite high diversity in the capsid viral protein (VP) sequence, the structural topologies of all parvoviral capsids are conserved. However, surface loops inserted between the core secondary structure elements vary in conformation that enables the assembly of unique capsid surface morphologies within individual genera. These variations enable each virus to establish host niches by allowing host receptor attachment, specific tissue tropism, and antigenic diversity. This review focuses on the diversity among the parvoviruses with respect to the transcriptional strategy of the encoded VPs, the advances in capsid structure-function annotation, and therapeutic developments facilitated by the available structures.

Keywords: Antibody interactions; Cryo-EM; Densovirus; Parvovirus; Receptor interactions; X-ray crystallography; single stranded DNA virus.

Figure 1

Evolutionary relationships of members of family Parvoviridae based on the conserved NS1 tripartite helicase domain. Branches of lineages highlighted in blue indicate the absence of a phospholipase A₂ (PLA₂) domain in the minor capsid viral protein, VP1. Capsid protein encoding gene homology is mapped as circles of different colors, where same colored circles indicate homologous genes (homology search defined, without the incorporation of the PLA₂ sequence, as whether a protein sequence gives a hit out of targeted 5000 sequences at an expectation value of 100 by the BlastP algorithm of the NCBI Blast application [2]). The size of the circle indicates the size of VP1 based on the scale to the left.

Figure 2

Cladogram of the subfamily Parvovirinae. The eight genera are shown. The general genome organization of each genus is shown in the middle with their ORF. The non-structural (NS) protein expressing genes ns or rep are simplified and only the ORF is shown. Below the cap ORF the transcripts for the expression of the individual VP are shown. On the right side the size and weight of the VPs are given. Note that the transcription profiles of the Aveparvovirus and Copiparvovirus genera have not been determined, and thus the sizes of the VPs are based on in silico predictions.

Figure 3

Cladogram of denso- and chapparvoviruses. The general genome organization and capsid protein expression strategy are shown. The ns genes are simplified and only the ORF is shown. The transcription strategy of members of genus Hepandensovirus, as well as of the new, unclassified starfish densoviruses, have not been determined, thus the sizes of the VPs are based on in silico predictions.

Figure 4

The N-termini of the major VPs of the Parvovirinae. For each genus a selection of available VP sequences are shown for the N-terminal 20–50 amino acids. All glycine residues are shown in red.

Figure 5

Disorder prediction for type members MVMp (red), BPV (pink), AAV2 (blue), and Parvovirus B19 (orange) VP1 by the PONDR_fit application [72]. Regions above 0.5 on the Y-axis are predicted to be disordered. Gray line drawings above the images indicate the approximate positions of the VPs. The regions highlighted in light blue indicate the locations of the surface exposed loops, the tops of which are defined as variable regions.

Figure 6

The structure of a VP monomer of CPV (PDB-ID: 2CAS). A cartoon ribbon diagram is shown. The beta strands (βA to βI, gray), α-helix A (red), interconnecting surface loops (with all secondary structure elements removed, green), and the N- and C-terminus are indicated. The approximate icosahedral 2-fold, 3-fold, and 5-fold axis are indicated by an oval, triangle, and pentagon, respectively. This image was generated using PyMOL [77].

Figure 7

The VRs of the Parvovirinae. (A) Structural superposition of VP monomers from different members of Protoparvovirus (left), Bocaparvovirus (center), and Dependoparvovirus. Individual colors for the ribbons are as indicated. The VRs: VR-I to VR-IX (or VR0 to VR8 for the protoparvoviruses), the DE, and HI loops are shown. (B) Location of the VRs, colored as indicated, on the capsid surface of MVMp as an example for Protoparvovirus (left), BPV for Bocaparvovirus (center), and AAV2 for Dependoparvovirus (right). The figures were generated using PyMOL [77].

Figure 8

Capsid structures of the Parvovirinae subfamily. A selection of capsid structures is shown for Protoparvovirus, Bocaparvovirus, Dependoparvovirus, and Erythroparvovirus. The capsid surfaces are viewed down the icosahedral 2-fold axes and are colored according to radial distance from the particle center (blue to red), as indicated by the scale bar. The capsid images were generated using Chimera [78]. In the lower right hand side, a symmetry diagram illustrating the positions of the icosahedral symmetry axes on the capsid surfaces is shown.

Figure 9

Parvovirinae-antibody complex structures. The highest resolution complex structures available for Protoparvovirus, Bocaparvovirus, Dependoparvovirus, and Erythroparvovirus are shown. The cryo-EM density maps are viewed down the icosahedral 2-fold axis and are colored according to radial distance from the particle center (blue to red), as indicated by the scale bar. The FAbs decorating the capsid surface are in red. The FAbs bind across the icosahedral 2-fold (e.g., CPV:FAbE), the 2-/5-fold wall (HBoV1:9G12), the 3-fold (AAV5:HL2476), and 5-fold depression (B19:hFab). The images were generated using Chimera [78]. (CPV: EMD-6629, B19: EMD-9110).

Figure 10

Disorder prediction for densoviruses. AdDV (blue), BmDV1 (pink), GmDV (green), and PstDV (black) VP1. The PONDR_fit application was utilized [72]. Regions above 0.5 on the Y-axis are predicted to be disordered. The approximate locations of the VPs are indicated in the grey bars above. In case of AdDV, both VP1 and VP2 have unique N-terminal regions. The regions highlighted in light blue in the disorder plot indicate the locations of the surface exposed loops, their apexes are VRs.

Figure 11

The N-termini of the major VPs of the Densovirinae. For each genus a selection of available VP sequences are shown for the N-terminal 20–50 amino acids. All glycine residues are in red.

Figure 12

The densovirus VP structure. (A) Cartoon ribbon diagrams of the ordered common VP structures of GmDV and AdDV (top), BmDV1 and PstDV (bottom). The first ordered N-terminal residue and C-terminal residue are labeled. The conserved β-core and αA helix are colored in black and labeled in GmDV. Loops and subloops within the large loops are as colored in the key at the bottom and EF and GH sub-loops are labeled. The approximate 5-fold symmetry axis is marked by a pentagon, the 3-fold by a triangle, and the 2-fold by an ellipsoid. (B) A GmDV VP structure (Ambidensovirus) superimposed on the VPs of AdDV (left), BmDV1 (middle), and PstDV (right). Conformational diversity on the surface loops is evident, especially between GmDV and BmDV, and GmDV and PstDV.

Figure 13

Multimeric interactions of densoviral and parvoviral VPs. (A) Ribbon cartoon diagrams of the interactions between βA and βB at the 2-fold symmetry axis of GmDV and CPV. The eight-stranded core, with the additional βA, which performs the domain swapping, are colored blue and black. (B) Interaction of three 3-fold symmetry related VPs for GmDV and CPV. The open annulus-like structure at the 3-fold axis of the densovirus trimer compared to the more closed arrangement in the vertebrate parvoviruses is evident. The triangle indicates the 3-fold axis and the pentagon the 5-fold axis.

Figure 14

Densoviral capsid structures. The capsid surface images of GmDV, AdDV, BmDV1, and PstDV. The resolution of each structure is in parenthesis. The AAV2 and CPV capsid images are shown for comparison. The scale bar shows the radial distance (from the capsid center) used for the images. An icosahedral symmetry diagram indicating the positions of the visible symmetry axes on the capsid images are shown at the bottom right hand side.

Figure 15

Overview of published parvoviral capsid structures since 1990. Structures determined by X-ray crystallography are shown in red and structures determined by cryo-EM in blue. Important milestones of structural parvovirology are indicated.