Re-refinement of the vault ribonucleoprotein particle

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.352 
  • R-Value Observed: 0.352 

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

Casanas, A.Querol-Audi, J.Guerra, P.Pous, J.Tanaka, H.Tsukihara, T.Verdaguer, N.Fita, I.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1054-1061

  • DOI: https://doi.org/10.1107/S0907444913004472
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major vault protein861Rattus norvegicusMutation(s): 0 
Find proteins for Q62667 (Rattus norvegicus)
Explore Q62667 
Go to UniProtKB:  Q62667
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62667
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.352 
  • R-Value Observed: 0.352 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 702.246α = 90
b = 383.796β = 124.69
c = 598.48γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations