Near-atomic structure of a giant virus

Abstract

Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have remained unknown. Here we describe a 3.5 Å resolution icosahedrally averaged capsid structure of Paramecium bursaria chlorella virus 1 (PBCV-1). This structure consists of 5040 copies of the major capsid protein, 60 copies of the penton protein and 1800 minor capsid proteins of which there are 13 different types. The minor capsid proteins form a hexagonal network below the outer capsid shell, stabilizing the capsid by binding neighboring capsomers together. The size of the viral capsid is determined by a tape-measure, minor capsid protein of which there are 60 copies in the virion. Homologs of the tape-measure protein and some of the other minor capsid proteins exist in other NCLDVs. Thus, a similar capsid assembly pathway might be used by other NCLDVs.

Fig. 1

Overall structure of the PBCV-1 capsid. a Icosahedrally averaged cryo-EM reconstruction of the viral capsid, colored according to the radial distance from the center of the virus. The boundaries of two neighboring trisymmetrons and two pentasymmetrons are outlined in black. The T number including the h and k vectors are indicated. b The cryo-EM density of the minor capsid proteins and the penton proteins after removing the outer capsid shell. Each protein is shown in a different color as indicated on the right. c Diagrammatic organization of the minor capsid proteins and capsomers viewed from inside the virus. The pseudo-hexameric capsomers are outlined. Each gray dot within each hexagon represents a Vp54 subunit. The icosahedral 3-fold and 2-fold axes are shown as solid black triangles and ovals, respectively. Different minor capsid proteins and the penton proteins are shown as different shapes with different colors, as indicated. Darker color is used in one icosahedral asymmetric unit. The pseudo-hexameric capsomers are labeled A, B, C, … in the trisymmetrons and a, b, c, … in the pentasymmetrons

Fig. 2

Structures of the penton protein (P1) and the MCPs. a Ribbon diagram of the penton protein. b Diagrammatic representation of the arrangement of β-strands in the penton protein. Residues are numbered at the ends of the β-strands. c Different conformational arrangements of the N terminus of the MCP. The Vp54 subunit structure of capsomer a (yellow) and capsomer b (magenta) are superimposed on the crystal structure of Vp54 (gray). Only the N-terminal 35 residues of each are shown for clarity

Fig. 3

Structures of the minor capsid proteins that glue together capsomers within each trisymmetron. Each minor capsid protein is rainbow colored from red at the C terminus to magenta at the N terminus. The neighboring capsomers are shown in gray and labeled as in Fig. 1c. a The minor capsid protein P2 (blue in Fig. 1c). Scale bar, 50 Å. b The three P3 molecules within one icosahedral asymmetric unit (red in Fig. 1c) and their neighboring capsomers. Scale bar, 50 Å. c Ribbon diagram of the three-helix bundle formed by the N-terminal parts of each P3 molecule around each icosahedral 3-fold axis. The icosahedral 3-fold axis is identified by a solid black triangle. Scale bar, 10 Å. d The minor capsid protein P5. Scale bar, 50 Å. e One of the four P4 molecules within an icosahedral asymmetric unit. Scale bar, 50 Å

Fig. 4

Structures of the minor capsid proteins that glue together capsomers within each pentasymmetron. The minor capsid proteins and their neighboring capsomers are shown as ribbon diagrams. All the capsomers are colored gray and labeled as in Fig. 1c. a Minor capsid proteins P6, P7, and P8. b Minor capsid protein P9. c Minor capsid protein P10. Scale bars, 50 Å

Fig. 5

Structures of minor capsid proteins P11, P12, P13, and P14. These proteins bind together neighboring symmetrons and/or have potential membrane association functions. All the structures are shown as ribbon diagrams. a The second, third, and fourth P11 molecule within an icosahedral asymmetric unit (see Fig. 1c) and their neighboring capsomers (gray). All the capsomers are labeled as in Fig. 1c. b Minor capsid proteins P12, P13, and P14. Scale bars, 50 Å