Fig 1.
Atomic model of capsid and CPs in GLV-HP and GLV-CAT.
The T = 1 capsid geometry and CP-A and CP-B organization in (A) GLV-HP and (H) GLV-CAT. Raw cryo-EM micrographs of (B) GLV-HP and (I) GLV-CAT. The close-up views of N-termini and C-termini in CP-A and CP-B are shown in (C–G) for GLV-HP and (J–N) for GLV-CAT.
Fig 2.
C-terminal extension structure of the CP–CP interface in the GLV-HP and GLV-CAT capsids.
The atomic model of the 5-fold CP complex of (A) GLV-HP (CP-A in green; CP-B in orange) and (C) GLV-CAT (CP-A in light blue; CP-B in pink) is shown from their inside view. The interlocking C-terminal extensions from CP-A to CP-B and those from CP-B to CP-A are highlighted in the surface representation. The close-up views of the interactions between the C-terminal extension and the adjacent capsid are shown in (B) for GLV-HP and in (D) and (E) for GLV-CAT. The amino acid residues involved in the interactions are indicated. The red dashed lines between the amino acid residues indicate predicted hydrogen bonds with their distances in Ångström.
Fig 3.
Structural comparison of the GLV CP with those of Totiviridae and toti-like viruses.
ScV-L-A, ScV-L-BC, and TVV2 CPs are shown in grey. The GLV and OmRV CPs are shown in orange and blue. The unique surface loops of the GLV and the OmRV CPs are shown as transparent surface representation. (A) The CP of GLV and OmRV that infects extracellularly is aligned with that of ScV-L-A, ScV-L-BC, and TVV2, which infect intracellularly. (B) Aligned CP structure of GLV and OmRV. The colored boxes, also shown as (a), (b), (c), and (d), indicate the surface regions of the extra loops that are identified in the GLV and OmRV CPs. (C) Close-up views of the extra loops. The box colors and regions correspond to those in (B). CP-B subunit of GLV-HP (PDB ID: 8R0F), OmRV-LZ (PDB ID: 7D0K), ScV-L-A (PDB ID: 1M1C), ScV-L-BC (PDB ID: 7QWX), and TVV2 (PDB ID: 7LWY) were utilized for the structural alignment.
Fig 4.
Pore structure of the GLV capsid.
A surface electrostatic potential map of the 5-fold CP complex of GLV-HP and GLV-CAT from outside and inside views is shown in red (negatively charged) and blue (positively charged) scales. A close-up view and cross-section of the pore structure and surface charges are also shown at the bottom.
Fig 5.
Lack of putative cap-snatching pockets in GLV and OmRV.
(A) Electrostatic surfaces of Totiviridae and toti-like virus CPs are shown in blue (positive) and red (negative) scales. The CP of the yeast Totiviridae viruses ScV-L-A and ScV-L-BC have cap-snatching active pockets and invariant His residues (His154 or His156) (yellow dotted circles). The CP of TVV2 is speculated to have a cap-snatching pocket with three putative His residues (His537, His648, and His658) in a position similar to that in the yeast Totiviridae viruses (yellow dotted circle). However, in the GLV and OmRV CPs, no His residue is observed on the corresponding cap-snatching pocket, although three His residues (His288, His387, His444) in the GLV CP and one His residue (His986) in the OmRV CP are exhibited on the surfaces. (B) Conserved helices and invariant His residue in Totiviridiae and toti-like viruses. A conserved helix-turn-helix and a long helix are highlighted as dotted circles and rectangles in each CP structure.
Fig 6.
Amino acid alterations and structural variability of CPs between GLV-HP and GLV-CAT.
(A) Amino acid alterations between GLV-HP and GLV-CAT are mapped on a GLV-HP CP-A/CP-B dimer. (B) Local RMSD values are calculated per amino acid residue. The RMSD values are scaled by blue (low RMSD) and red (high RMSD). The yellow pentagon indicates the 5-fold axis of the GLV capsid. (C) Intra-subunit interaction of Phe230 of CP-B in the GLV-HP capsid. (D) Inter-subunit interaction between CP-A and Leu320 of CP-B in the GLV-CAT capsid.