Extended Data Fig. 2: Image processing of HTLV-1 Gag VLPs.

a) Image processing workflow for the subtomogram averaging and multiparticle refinement of the CA layer from HTLV-1 Gag-based VLPs. See Methods for more details. b) XZ-slices through bin4 averages of the immature HTLV-1 Gag lattice, showing the varying distance of the CA-layer with respect to the viral membrane (VM). The distance was measured from the outer VM layer to the electron-lucent layer between CA-NTD and CA-CTD. c) Histogram showing the measured distances of the CA-layer to the viral membrane. The distance was determined by re-aligning particles to viral membrane layers. The individual CA-membrane distances then correspond to the mean value + particle Z-shift. N = 51,700. d) Fourier-shell correlation (FSC) for the independently aligned CA-NTD (blue line) and CA-CTD layer (red line), showing a resolution of 5.9 Å and 6.2 Å at the 0.143 criterion, respectively.e) Local resolution measurements for the two cryo-EM density maps generated by focusing either on the CA-NTD (top) or the CA-CTD (bottom). The color code for the local resolution in Å is shown below. The maps are shown in two views, once as seen from the outside of the VLP (left) and in a side view (right). The viral membrane (VM), the CA-NTD, and CA-CTD are annotated in the side view. The CA hexamer center is indicated with a small black hexagon. f) Model of HTLV-1 CA-NTD (cyan) and CA-CTD (orange) rigid-body fitted into a composite map of the immature HTLV-1 CA lattice and shown from two views (as seen from the outside of the VLP on the top, and a side view on the bottom). The density of the CA-NTD is from the cryo-electron microscopy density map refined on the CA-NTD (EMD-17942) and the density for the CA-CTD from EMD-17943). The CA hexamer center is indicated with a small black hexagon.