4V60

The structure of rat liver vault at 3.5 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.311 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 384-388

  • DOI: 10.1126/science.1164975
  • Primary Citation of Related Structures:  
    4V60

  • PubMed Abstract: 
  • Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3 ...

    Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3.5 angstrom resolution and show that the cage structure consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain, and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells.


    Related Citations: 
    • A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry
      Kato, K., Tanaka, H., Sumizawa, T., Yoshimura, M., Yamashita, E., Iwasaki, K., Tsukihara, T.
      (2008) Acta Crystallogr D Biol Crystallogr 64: 525

    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major vault protein
A, B, C, D, E, F, G, H
861Rattus norvegicusMutation(s): 0 
Gene Names: Mvp
UniProt
Find proteins for Q62667 (Rattus norvegicus)
Explore Q62667 
Go to UniProtKB:  Q62667
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.311 
  • 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
MOSFLMdata reduction
DMmodel building
CNSrefinement
RAVEmodel building
SCALAdata scaling
DMphasing
RAVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other