Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues. Despite a lack of sequence similarity between the two proteins, they have a similar α-helical domain, the structural signature shared with the lineage of the dsRNA bluetongue virus-like viruses. Domain insertions in P2 and P4 preferential sites provide additional functions at the capsid outer surface, probably related to enzyme activity. The P2 insertion has a fold similar to that of gelsolin and profilin, two actin-binding proteins with a function in cytoskeleton metabolism, whereas the P4 insertion suggests protease activity involved in cleavage of the P2 383-residue C-terminal region, absent in the mature viral particle. Our results indicate that the intimate virus-fungus partnership has altered the capsid genome-protective and/or receptor-binding functions. Fungal virus evolution has tended to allocate enzyme activities to the virus capsid outer surface.

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Published in PLOS Pathogens, v. 13, 12, e1006755, p. 1-20.

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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This work was supported by grants from the Spanish Ministry of Economy and Competitivity (BFU2013-43149-R to DL and JMR, BFU2014-54181 to JLC and BFU2014-55475-R to JRC), the Madrid regional government (S2013/MIT-2850 to JLC and S2013/MIT-2807 to JRC), the Japanese Ministry of Education, Culture, Sports, Science, and Technology (KAKENHI 25252011 and 16H06436, 16H06429, and 16K21723 to NS), and the NIH Intramural Research Program, Center for Information Technology (to BLT). The CNB-CSIC Proteomics Facility, which belongs to ProteoRed, PRB2-ISCIII, was supported by “Instituto de Salud Carlos III” (ISCIII) grant PT13/000. CPM was a PhD fellow of the La Caixa Foundation International Fellowship Program (La Caixa/CNB).

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The RnQV1-W1118 cryo-EM map is deposited in the Electron Microscopy Data Bank (accession no. emd-3619) and the atomic coordinates of the RnQV1-W1118 P2 and P4 proteins are deposited in the PDB (ID code 5ND1).

journal.ppat.1006755.s001.tif (6057 kB)
S1 Fig. Resolution of the RnQV1capsid and quality of the RnQV1 P2 and P4 density maps.

journal.ppat.1006755.s002.tif (473 kB)
S2 Fig. Mass spectra of P2 and P4.

journal.ppat.1006755.s003.tif (594 kB)
S3 Fig. Structural similarity of P2 and P4 SIID.

journal.ppat.1006755.s004.tif (795 kB)
S4 Fig. Structural alignment of P2 with PcV domain A and L-A virus Gag CP.

journal.ppat.1006755.s005.tif (772 kB)
S5 Fig. Structural alignment of P4 with PcV domain A and L-A virus Gag CP.

journal.ppat.1006755.s006.tif (6320 kB)
S6 Fig. dsRNA virus T = 1 inner capsid surfaces with electrostatic potentials.

journal.ppat.1006755.s007.tif (4373 kB)
S7 Fig. C-terminal P4 density occludes the five-fold axis channels of the RnQV1 capsid.

journal.ppat.1006755.s008.tif (3654 kB)
S8 Fig. Proposed assembly intermediates for 120-subunit immature RnQV1 capsid.

journal.ppat.1006755.s009.docx (86 kB)
S1 Table. Analysis by MALDI-TOF/TOF MS and MS/MS of P2 and P4 proteins.

journal.ppat.1006755.s010.mp4 (3657 kB)
S1 Movie. Structural alignment of RnQV1 capsid proteins P2 and P4, showing superimposed α-helices and β-strands, rainbow-colored from blue (N terminus) to red (C terminus) for each protein (insertions or non-superimposed regions, white).

journal.ppat.1006755.s011.mp4 (4429 kB)
S2 Movie. Structural alignment of P2 and P4 SIID, showing superimposed α-helices and β-strands, rainbow-colored from blue (N terminus) to red (C terminus) for each domain.

journal.ppat.1006755.s012.mp4 (8555 kB)
S3 Movie. Structural alignment of P2 Asp227-Tyr350 domain with gelsolin, profilin, and the ferredoxin-like domain, showing superimposable β-sheet and α-helices.

journal.ppat.1006755.s013.mp4 (8601 kB)
S4 Movie. The P2 C-terminal segment is located on the P4 outer surface, and the last C-terminus residue (Gly973) ends in a P4 surface crevice.

journal.ppat.1006755.s014.mp4 (6121 kB)
S5 Movie. Structural alignment of P2 (left) and P4 (right) with PcV domain A (center), showing superimposable α-helices and β-strands, rainbow-colored from blue (N terminus) to red (C terminus).

journal.ppat.1006755.s015.mp4 (6183 kB)
S6 Movie. Structural alignment of P2 (left) and P4 (right) with L-A virus Gag CP (center), showing superimposable α-helices and β-strands, rainbow-colored from blue (N terminus) to red (C terminus).