2QZV

Draft Crystal Structure of the Vault Shell at 9 Angstroms Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.00 Å
  • R-Value Work: 0.615 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Draft crystal structure of the vault shell at 9-A resolution.

Anderson, D.H., Kickhoefer, V.A., Sievers, S.A., Rome, L.H., Eisenberg, D.

(2007) PLoS Biol 5: e318-e318

  • DOI: 10.1371/journal.pbio.0050318
  • Primary Citation of Related Structures:  
    2QZV

  • PubMed Abstract: 

    • Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized ...

    Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMVP vaults), diffracting to about 9-A resolution. The asymmetric unit contains a half vault of molecular mass 4.65 MDa. X-ray phasing was initiated by molecular replacement, using density from cryo-electron microscopy (cryo-EM). Phases were improved by density modification, including concentric 24- and 48-fold rotational symmetry averaging. From this, the continuous cryo-EM electron density separated into domain-like blocks. A draft atomic model of cpMVP was fit to this improved density from 15 domain models. Three domains were adapted from a nuclear magnetic resonance substructure. Nine domain models originated in ab initio tertiary structure prediction. Three C-terminal domains were built by fitting poly-alanine to the electron density. Locations of loops in this model provide sites to test vault functions and to exploit vaults as nanocapsules.

    Related Citations: 
    • Cryoelectron Microscopy Imaging of Recombinant and Tissue Derived Vaults: Localization of the Mvp N Termini and Vparp
      Mikyas, Y., Makabi, M., Raval-Fernandes, S., Harrington, L., Kickhoefer, V.A., Rome, L.H., Stewart, P.L.
      (2004) J Mol Biol 344: 91
    • Solution structure of a two-repeat fragment of major vault protein
      Kozlov, G., Vavelyuk, O., Minailiuc, O., Banville, D., Gehring, K., Ekiel, I.
      (2006) J Mol Biol 356: 444
    Organizational Affiliation: 

    Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California, United States of America.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major vault proteinA, B873Rattus norvegicusMutation(s): 0 
Gene Names: Mvp
UniProt
Find proteins for Q62667 (Rattus norvegicus)
Explore Q62667 
Go to UniProtKB:  Q62667
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62667
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 9.00 Å
  • R-Value Work: 0.615 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 631.449α = 90
b = 464.724β = 123.84
c = 584.572γ = 90
Software Package:
Software NamePurpose
DMmodel building
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
DMphasing
CNSrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance