4V60

The structure of rat liver vault at 3.5 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 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:  2ZUO, 2ZV4, 2ZV5
  • Also Cited By: 4HL8

  • 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 th ...

    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.,Sect.D 64: 525


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major vault protein
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m
861Rattus norvegicusGene Names: Mvp
Find proteins for Q62667 (Rattus norvegicus)
Go to UniProtKB:  Q62667
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 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 = 90.00
b = 383.796β = 124.69
c = 598.480γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
RAVEphasing
RAVEmodel building
DMphasing
CNSrefinement
SCALAdata scaling
DMmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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