Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C39  (3D View)
Global Stoichiometry: Homo 39-mer - A39 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 95.92 kDa 
• Atom Count: 6157 
• Modelled Residue Count: 782 
• Deposited Residue Count: 861 
• Unique protein chains: 1

4HL8

Re-refinement of the vault ribonucleoprotein particle

• PDB DOI: 10.2210/pdb4HL8/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2012-10-16 Released: 2013-06-05 
• Deposition Author(s): Casanas, A., Querol-Audi, J., Guerra, P., Pous, J., Tanaka, H., Tsukihara, T., Verdaguer, V., Fita, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.354 
• R-Value Work: 0.352 
• R-Value Observed: 0.352 

Literature

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

• PubMed: 23695250 
• DOI: 10.1107/S0907444913004472
• Primary Citation of Related Structures:  
  4HL8


• 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.

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Related Citations: 

• The structure of rat liver vault at 3.5 angstrom resolution.
  Tanaka, H., Kato, K., Yamashita, E., Sumizawa, T., Zhou, Y., Yao, M., Iwasaki, K., Yoshimura, M., Tsukihara, T.
  (2009) Science 323: 384

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major vault protein	A	861	Rattus norvegicus	Mutation(s): 0  Gene Names: Mvp
UniProt
Find proteins for Q62667 (Rattus norvegicus) Explore Q62667  Go to UniProtKB:  Q62667

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 702.246	α = 90
b = 383.796	β = 124.69
c = 598.48	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-16 
• Released Date: 2013-06-05 
Deposition Author(s): Casanas, A., Querol-Audi, J., Guerra, P., Pous, J., Tanaka, H., Tsukihara, T., Verdaguer, V., Fita, I.

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release