Fig. 8: Modelling high-resolution features in bDENV-2.
a A cartoon representation of the bDENV-2 structure coloured by domain according to the domain diagram below. The N-linked glycans are shown in cyan. b Zooms of the density (mesh) and fit of the bDENV-2 structure (purple sticks). Water molecules are shown as red spheres. c Overlay of E-H3 of bDENV-2 (purple) and DENV-2 (green, PDB: 3J27). Side chains are represented as sticks and the main chain as a cartoon. d Orthogonal views of the E dimer. Out of ~150 water molecules, 59 are conserved in all prM-E heterodimers within the particle and are represented as cyan dotted spheres. When compared to a crystal structure of similar resolution (PDB: 3C5X), 11 are conserved and are represented as solid, magenta spheres. The inset represents a zoom on the fusion loop highlighting a conserved water molecule. Water molecules are shown as red and green spheres for the cryo-EM structure and crystal structure, respectively. e A cartoon representation of an E–M dimer in bDENV-2 (magenta) subtracted from the reconstruction to produce a difference map (purple). The difference map was low-pass filtered for clarity and the density surrounding the two lipid molecules is highlighted (yellow and green). f A comparison of the density near the pocket factors in bDENV-2, bMVEV, bWNVKUN, WNVKUN, ZIKV (EMD-7543, PDB: 6CO8) and TBEV (EMD-3752, PDB: 5O6A). The structure of the E protein and surrounding density is displayed in magenta. The structure of the lipids from bDENV-2 is displayed in each panel as sticks (green and yellow) and density within 2 Å is coloured accordingly.
