Extended Data Fig. 1: Characterisation of digitonin-permeabilized CEM cells and isolated HIV-1 cores.
a, Schematic of viral core and permeabilized T cell preparations. b, Representative confocal microscopy images of digitonin-permeabilized CEM cells incubated with 500 kDa FITC-dextran. Channels shown include transillumination, FITC-dextran, SiR-DNA, and a merged image of SiR-DNA with FITC-dextran. Scale bar = 10 μm. c, mNeonGreen-IN labelled HIV-1 core bands after ‘spin-thru’ detergent treatment. The red arrowhead indicates the top band extracted for this study, while the green band below represents aggregated cores, which were discarded. d, Representative electron micrographs of isolated HIV-1 cores derived from WT, E45A, E45A/R132T, and N74D variants. Scale bar = 100 nm. e, A bar chart illustrating the composition of all input core shapes in each sample. Cone-shape cores are in purple and tube-shaped cores are in blue. f, A violin plot of the statistical analysis on the size of all input cone-shaped cores (width measured at the wide end) in each state. The size of cone-shaped virion cores measures 56.79 ± 4.935 nm (SE = 0.3678, n = 180), the WT measure 57.71 ± 4.758 nm (SE = 0.4644, n = 105), the E45A measures 57.89 ± 8.162 nm (SE = 0.5845, n = 195), the E45A/R132T measures 58.66 ± 9.166 nm (SE = 0.7560, n = 147), and the N74D measures 56.46 ± 6.644 nm (SE = 0.5052, n = 173). White lines represent the medians, black lines represent the quartiles, and black dots represent individual cone-shaped HIV-1 cores (One-way ANOVA test for all, ns = no significance). g, A violin plot of the statistical analysis on the size (width measured) of all input tube-shaped cores in each state. The size of tube-shaped HIV-1 virion cores measures 41.91 ± 5.056 nm (SE = 0.8672, n = 34), the WT measure 42.27 ± 2.875 nm (SE = 0.5996, n = 23), the E45A measures 42.84 ± 3.116 nm (SE = 0.4751, n = 44), the E45A/R132T measures 42.63 ± 3.460 nm (SE = 0.5688, n = 37), and the N74D measures 43.40 ± 3.590 nm (SE = 0.7655, n = 23). White lines represent the medians, black lines represent the quartiles, and black dots represent individual tube-shaped HIV-1 cores (One-way ANOVA test for all, ns = no significance). Panel a created with BioRender.com.
