Fig. 7
Final reconstruction analysis of compact and expanded CVB1-VLPTween80 obtained by cryoEM and single-particle reconstruction. (A) Final reconstructions shown as surface at 2.5σ above mean with fitted model (left) and the atomic model with unmodeled density in red (right). Unmodeled densities and positions of interest are marked with circles and are coded with small letters. (B) Focused view on the hydrophobic pocket (at position p on A) housing a lipid factor represented as palmitate in compact CVB1-VLPTween80. Density map is shown as mesh at 2.5σ above mean. (C) Focused view on the expanded CVB1-VLPTween80 density map on the site which corresponds to position in B). The pocket in the expanded particles is collapsed and there is no density corresponding to a lipid factor. Density map is shown as mesh at 2.5σ above mean. (D) Focused view on the interprotomer pocket (position d on A) of compact CVB1-VLPTween80 and native CVB1 (PDB ID 7DPF) located at the interface of two asymmetric subunits between VP1 and VP3 as shown on the right. Unmodeled density present in the interprotomer pocket of CVB1-VLPTween80 is shown as mesh at 2.5σ above mean on the left. On the right one asymmetric subunit is shown as surface at 2.5σ above mean with the unmodeled density in green. (E) – G) Focused views on the helices around the 2-fold symmetry axis and the VP3 loop of compact (E) and expanded (F) CVB1-VLPTween80 and expanded CVB1 (G) at position as shown in F). H) Focused view down the 3-fold symmetry axis. The density map is shown as mesh at 2.5σ above mean showing the unmodeled density between Ds of VP3 (positions i1 and i2 in A).
