4HL8

Re-refinement of the vault ribonucleoprotein particle

Summary for 4HL8

• Entry DOI: 10.2210/pdb4hl8/pdb
• Related: 2ZUO 3GNF
• Descriptor: Major vault protein (1 entity in total)
• Functional Keywords: 9 repeat domains, protein-protein complex, ribonucleoprotein, structural protein, cytoplasmic
• Biological source: Rattus norvegicus (brown rat,rat,rats)
• Cellular location: Cytoplasm: Q62667
• Total number of polymer chains: 1
• Total formula weight: 95920.11

Authors

Casanas, A.,Querol-Audi, J.,Guerra, P.,Pous, J.,Tanaka, H.,Tsukihara, T.,Verdaguer, V.,Fita, I. (deposition date: 2012-10-16, release date: 2013-06-05, Last modification date: 2024-02-28)

Primary citation

Casanas, A.,Querol-Audi, J.,Guerra, P.,Pous, J.,Tanaka, H.,Tsukihara, T.,Verdaguer, N.,Fita, I.
New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach.
Acta Crystallogr.,Sect.D, 69:1054-1061, 2013

PubMed 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.

PubMed: 23695250
DOI: 10.1107/S0907444913004472

Experimental method

X-RAY DIFFRACTION (3.5 Å)