The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses
- Center for Cooperative Research in Biosciences, Spain
- Centro de Edafología y Biología Aplicada del Segura, Spain
- Consejo Superior de Investigaciones Científicas, Spain
- Columbia University, United States
Figures
Figure 1 with 6 supplements
CryoEM structure of PepMV and atomic model for its CP.
(A, B) Renderings of the 3D density map for PepMV that displays a left-handed helical symmetry with 34.6 Å of helical pitch (P). The map is seen segmented domain-wise. The cut-away view (B) reveals …
Figure 1—figure supplement 1
Electron micrograph of PepMV cryoEM data.
Field of an electron micrograph showing several PepMV virions. The black boxes correspond to straight segments of the helices selected for further data processing. PepMV,Pepino mosaic virus.
Figure 1—figure supplement 2
Helical symmetry search.
Search for helical symmetry parameters obtained in Spring package (Desfosses et al., 2014). Several 3D maps with different helical symmetry parameters are calculated starting with bi-dimensional …
Figure 1—figure supplement 3
Estimation of resolution for the cryoEM map of PepMV virions.
Fourier Shell Correlation (FSC) calculated between 3D maps from two fully independently processed halves of the data set (brown line) and between the atomic model and the cryoEM map (green line). …
Figure 1—figure supplement 4
Local resolution measurement in isolated PepMV CP subunit.
Segmented density for a single PepMV CP subunit is rendered in two orientations showing the estimated local resolution. The calculations were performed with the raw cryoEM map, but only one PepMV CP …
Figure 1—figure supplement 5
Comparison between modeled PepMV CP and the atomic structure of PapMV CP.
(A) Comparison between the built atomic model for PepMV CP (colored domain wise as in Figure 1) and the reported structure for the truncated version of PapMV CP (colored grey; pdb code 1DOX (Yang et …
Figure 1—figure supplement 6
Table of some figures of merit for the structure of the modeled PepMV CP.
Short table with figures of merit calculated in Molprobity for the validation of the atomic model of PepMV CP. PepMV CP, Pepino mosaic virus coat protein
Figure 2 with 3 supplements
Interaction between PepMV CP and ssRNA.
(A) Cut-away rendering of four PepMV CP subunits at consecutive turns of the helix with the ssRNA between them. Molecular surfaces are colored according to their electrostatic potential using a …
Figure 2—figure supplement 1
Rendering of the atomic model construction used during MDFF for the analysis of the protein-RNA interfaces.
Representation of four PepMV subunits and two molecules of ssRNA obtained after MDFF. The set was chosen to explore protein–protein and protein–RNA interactions. CP1 and CP4 also contain the …
Figure 2—figure supplement 2
Progress during the MDFF run.
Progress of the MDFF measured as the improvement of the cross-correlation between the atomic coordinates (shown in Figure 2—figure supplement 1) and the cryoEM map for PepMV along the 40 ns of the …
Figure 2—figure supplement 3
Sequence alignment between CP from several representatives of the genus Potexvirus.
The alignment was produced by CLC Main Workbench and indicates the degree of conservation and the consensus sequence. The alignment includes CP sequences from: Pepino mosaic virus (PepMV) …
Figure 3
Interactions through N- and C-terminal flexible regions mediate PepMV assembly.
(A) Ni subunit links to a hydrophobic groove in the Ni-1 subunit via the N-terminal arm. (B) In the Ni-1 subunit a pocket of hydrophobic residues allocates F28 from the Ni adjacent subunit. (C) …
Figure 4
Structural homology between PepMV CP and NP from phleboviruses.
(A–D) The atomic structures for the modeled PepMV CP and for the NP from RVFV (pdb code 4H5O (Raymond et al., 2012) are depicted in similar orientations. The representations include the respective …
