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 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/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. 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
Major vault protein
A, B
873Rattus 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
Sequence Annotations
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  • 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

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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
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description