New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach

Abstract

The vault particle, with a molecular weight of about 10 MDa, is the largest ribonucleoprotein that has been described. The X-ray structure of intact rat vault has been solved at a resolution of 3.5 Å [Tanaka et al. (2009), Science, 323, 384-388], showing an overall barrel-shaped architecture organized into two identical moieties, each consisting of 39 copies of the major vault protein (MVP). The model deposited in the PDB includes 39 MVP copies (half a vault) in the crystal asymmetric unit. A 2.1 Å resolution structure of the seven N-terminal repeats (R1-7) of MVP has also been determined [Querol-Audí et al. (2009), EMBO J. 28, 3450-3457], revealing important discrepancies with respect to the MVP models for repeats R1 and R2. Here, the re-refinement of the vault structure by incorporating the high-resolution information available for the R1-7 domains, using the deformable elastic network (DEN) approach and maintaining strict 39-fold noncrystallographic symmetry is reported. The new refinement indicates that at the resolution presently available the MVP shell can be described well as only one independent subunit organized with perfect D39 molecular symmetry. This refinement reveals that significant rearrangements occur in the N-terminus of MVP during the closing of the two vault halves and that the 39-fold symmetry breaks in the cap region. These results reflect the highly dynamic nature of the vault structure and represent a necessary step towards a better understanding of the biology and regulation of this particle.

Direct visualization of vaults within intact cells by electron cryo-tomography

“…Vaults did not appear to adopt a preferred orientation within the granule beds, but a few vaults appeared to interact with granules at their caps, or by opening up at their waist region (Fig. 6), observations consistent with previous reports [8, 26]. Given the previously reported localization of vPARP to the waist region of the vault [1], it is possible that the granules are enzymatically targeted by vault-associated vPARP.…”

“…2, panels a, e). These observations underscore the role of the midsection in mediating vault dynamics, and are not surprising since the twofold axis at the vault waist region delineates the half-vault structures that comprise the full particle [8, 26]. Previous work suggested that within cells half-vaults could exchange with each other by separating at the midsection [27], but we did not see structures consistent with this type of complex dynamic.…”

“…Nine structural repeat domains within the MVP stack to form the “barrel” part of the vault, while a αβ globular domain defines its shoulder region. The distinctive cap structure at the end of the particle is formed by an extended α-helix with a unique C-terminal U-shaped fold [8, 9]. The joining of two half-vault structures encloses approximately 5 × 10 4 nm 3 [2], a volume sufficient to hold 2–3 ribosomes.…”

Notes of a protein crystallographer: the beauty of rose windows and the different meanings of symmetry

“…5b). The structure and some of the details of the function of these fascinating vault-like particles have been revealed by the groups of Tsukihara and coworkers in Japan (Tanaka et al, 2009) and Fita, Verdaguer and coworkers in Barcelona, Spain (Querol-Audí et al, 2009;Casañ as et al, 2013).…”

Reconstruction of Stochastic 3D Signals With Symmetric Statistics From 2D Projection Images Motivated by Cryo-Electron Microscopy

“…An important characteristic of many systems is symmetry, i.e., the electron scattering intensity is invariant under the operations of a symmetry group. On 05 November 2017, the Protein Data Bank [40] contained 130,005 structures in seven symmetry classes: Asymmetric (60.198%), Cyclic C n (31.020% with n ranging from 2 to 39 [41], [42] ), Dihedral D n (7.517% with n ranging from 2 to 48 [43]), Icosahedral I (0.491%), Tetrahedral T (0.280%), Octahedral O (0.248%), and Helical (0.245%). We focus on the rotational point groups, which are I, O, T , C n , and D n , and which have 60, 24, 12, n, and 2n symmetry operations, respectively.…”