Structural flexibility of the human vault protein revealed by high-resolution cryo-EM and molecular dynamics simulations

Lapenta, F.; Palacio-Rodriguez, K.; Cruz, S.; Marrancone, S.; Aupic, J.; Marechal, N.; Durand, A.; Moussaoui, D.; Covaceuszach, S.; Gangupam, B.; D'Ercole, C.; Parra, C.; Davide, C.; Tomaino, G.; Tortora, P.; de Marco, A.; Cassetta, A.; Magistrato, A.; Hummer, G.

doi:10.1101/2025.08.26.672097

bioRxiv · 10.1101/2025.08.26.672097

Structural flexibility of the human vault protein revealed by high-resolution cryo-EM and molecular dynamics simulations

Lapenta, F.·Palacio-Rodriguez, K.·Cruz, S.·Marrancone, S.·Aupic, J.·Marechal, N.·Durand, A.·Moussaoui, D.·Covaceuszach, S.·Gangupam, B.·D'Ercole, C.·Parra, C.·Davide, C.·Tomaino, G.·Tortora, P.·de Marco, A.·Cassetta, A.·Magistrato, A.·Hummer, G.

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Abstract

Vaults are massive ribonucleoprotein complexes, highly conserved and abundant in eukaryotic cells, yet with unclear function. Their thin-walled barrel-shape architecture is composed of two symmetrical, antiparallel half-shells, each containing 39 copies of the major vault protein (MVP). The spacious lumen of the vault suggests a role in cellular transport. To facilitate cargo encapsulation and release, the vault is thought to open into two halves, yet the molecular mechanism governing vault opening remains elusive. Here, we combine cryogenic electron microscopy (cryo-EM) and multi-scale molecular dynamics (MD) simulations to reveal the structural factors giving flexibility to the human vault protein. Using cryo-EM, we identified two alternative conformational states of the human vault, along with the half-vault shell. MD simulations of these structures show extensive, breathing-like motions, porous solvent-exposed surfaces, and distinct structural variability between conformational states. The stable intermediates and the flexibility at the interface of the half vaults together suggest a possible mechanism for the dynamic assembly and disassembly of the vault.

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Lapenta, F., Palacio-Rodriguez, K., Cruz, S., Marrancone, S., Aupic, J., Marechal, N., Durand, A., Moussaoui, D., Covaceuszach, S., Gangupam, B., D'Ercole, C., Parra, C., Davide, C., Tomaino, G., Tortora, P., de Marco, A., Cassetta, A., Magistrato, A., Hummer, G.. 2025-08-26. Structural flexibility of the human vault protein revealed by high-resolution cryo-EM and molecular dynamics simulations. https://doi.org/10.1101/2025.08.26.672097

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