Nuclear pores constrict upon energy depletion

Abstract

Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins that form an intricate cylindrical architecture around an aqueous central channel. This architecture is highly dynamic in space and time. Variations in NPC diameter were reported, but the physiological circumstances and the molecular details remain unknown. Here we combined cryo-electron tomography and subtomogram averaging with integrative structural modeling to capture a molecular movie of the respective large-scale conformational changes in cellulo. While actively transporting NPCs adopt a dilated conformation, they strongly constrict upon cellular energy depletion. Fluorescence recovery after photo bleaching experiments show that NPC constriction is concomitant with reduced diffusion and active transport across the nuclear envelope. Our data point to a model where the energy status of cells is linked to the conformation of NPC architecture.

Cone-shaped HIV-1 capsids are transported through intact nuclear pores

“…We found that the NPCs dilated to similar diameters in non-infected T cells ( Figure 6 D). Taken together, our findings indicate that the NPC structure observed under the relevant conditions, namely in infected and non-infected T cells in situ , is representative of the transporting state, whereas the constricted state observed in isolated nuclear envelopes ( von Appen et al., 2015 ) may be more relevant to stress conditions ( Zimmerli et al., 2020 ). In conclusion, our data show that the inner diameter of the central channel exceeds the dimensions of the broad end of intact HIV-1 capsids (∼55–60 nm) by ∼4–9 nm, rendering the nuclear entry of intact capsids geometrically possible.…”

“…The remaining 299 subtomograms from non-infected cells were aligned to pursue measurements of NPC diameters but not further processed. Measurements of NPCs diameter from outer-inner nuclear membrane fusions and inner ring were carried out from the asymmetric unit using in-house MATLAB scripts ( https://doi.org/10.5281/zenodo.4266419 ) ( Zimmerli et al., 2020 ).…”

Integrative structural modelling of macromolecular complexes using Assembline

“…No reuse allowed without permission. Finally, p-values are calculated from the cross-correlation scores of alternative fits as published before 7,21,24,29,31,32 . Briefly, the cross-correlation scores are first transformed to z-scores (Fisher's z-transform 33 ) and centered, from which two-sided p-values are computed using standard deviation derived from an empirical null distribution (derived from all obtained unique fits and fitted using fdrtool R-package 34 ).…”

“…The copyright holder for this preprint (which this version posted April 6, 2021. ; https://doi.org/10.1101/2021.04.06.438590 doi: bioRxiv preprint --traj --models --prefix 0000000 \ -o out/refinement/"$model_id"/out \ out/refinement/"$model_id"/config_refine.json \ params_refine.py \ rm -r out/refinement/"$model_id"/out 40. Analyze the output from the modelling by refinement by following the exact procedure described from step 21 up to step 31 (i.e., repeat steps [21][22][23][24][25][26][27][28][29][30][31], but now generating the scores using the command: extract_scores.py --multi…”

“…Integrating data from different techniques allows building models at a higher precision than using a single technique alone 8,19,20 . Multiple structures of macromolecular complexes have been obtained this way, even under in-cell conditions 8,7,21 .…”