Fig. 3: Remodelling of NPCs during HIV-1 core import.

a, A violin plot of the size distribution of PS-CEM NPCs with WT cores (purple; 95.22 ± 4.362 nm, s.e. = 0.5453, n = 64) and without cores (pink; 93.39 ± 4.315 nm, s.e. = 0.3756, n = 132). White lines represent the medians, black lines represent the quartiles and dots represent individual NPCs. Significance was determined using a two-sided t-test for one comparison; **P = 0.0062. b, Examples of occupied NPCs in which the eight subunits are well identified with high cross-correlation and correct orientation by template matching. Top: the six tomographic slices ((i)–(vi)) of WT cores traversing through the NPC. Middle: symmetry analysis by rotation based on the refined coordinates of each subunit. Bottom: mapped-back model of each NPC occupied by WT cores, using an adapted EM map EMD-51631 for better illustration. The WT cores and NPCs are labelled (indicated by white circles in the top view in some cases). The nucleus, NE and membranes are annotated accordingly. Scale bars, 50 nm. c–e, Violin plots of the included angles between adjacent subunits in PS-CEM NPCs (n = 43) occupied by WT cores (c), empty PS-CEM NPCs (n = 95) (d) and in-cell empty CEM NPCs (n = 42) (e). Bottom right inset (c): the measurement of the included angles. The thresholds (red dashed lines) are set at 47.5° (top) and 42.5° (bottom), deviating from the 8-fold symmetry reference angle of 45° (green dashed lines). The black violin units indicate deformed NPCs, white violin units indicate regular NPCs and dots represent included angles measured in individual NPCs. Top inset (c): deformed NPCs are grouped to the left side (purple background) of the charts for ease of comparison. For empty PS-CEM NPCs, purple violin units indicate NPCs associated with WT cores (docking and just-imported cores). f, A bar chart depicting the distribution of NPCs in the aforementioned three conditions. Significance was determined using a two-sided Fisher’s exact test for each pair; for occupied versus empty, P = 0.0050; for occupied versus in-cell empty, P = 0.0024; and for empty versus in-cell empty, P = 0.4983 (not significant (NS)). g, A bar chart depicting the distribution of core-associated NPCs in regular and deformed empty NPCs. Significance was determined using a two-sided Fisher’s exact test for 1 comparison; P = 0.4570. h, A violin plot of the statistical analysis on the size of WT cores (width measured at the wide end) in regular and deformed occupied NPCs. The size of WT cores in regular occupied NPCs measures 55.32 ± 4.854 nm (s.e. = 1.035, n = 22), and the size of WT cores in deformed occupied NPCs measures 55.05 ± 6.960 nm (s.e. = 1.519, n = 21). The white and black lines represent the medians, purple lines represent the quartiles and dots represent individual WT cores. Significance was determined by two-sided t-test for one comparison; NS. i, A violin plot of the statistical analysis on the size of NPCs occupied by WT cores. The regular NPCs measure 95.74 ± 1.684 nm (s.e. = 0.3591, n = 22) and the deformed NPCs measure 95.95 ± 4.841 nm (s.e. = 1.056, n = 21). The white and black lines represent the medians, purple lines represent the quartiles and dots represent individual occupied NPCs. Significance was determined by two-sided t-test for one comparison; NS. ONM–INM, outer nuclear membrane–inner nuclear membrane.