2QZV
Draft Crystal Structure of the Vault Shell at 9 Angstroms Resolution
Summary for 2QZV
| Entry DOI | 10.2210/pdb2qzv/pdb |
| Related | 1Y7X |
| Descriptor | Major vault protein (1 entity in total) |
| Functional Keywords | nanocapsule, barrel self-assembled from 96 staves, major vault protein, cytoplasm, ribonucleoprotein, structural protein, innate immunity |
| Biological source | Rattus norvegicus (Norway rat) |
| Cellular location | Cytoplasm: Q62667 |
| Total number of polymer chains | 2 |
| Total formula weight | 193862.72 |
| Authors | Anderson, D.H.,Kickhoefer, V.A.,Sievers, S.A.,Rome, L.H.,Eisenberg, D. (deposition date: 2007-08-17, release date: 2007-12-04, Last modification date: 2024-04-03) |
| Primary citation | Anderson, D.H.,Kickhoefer, V.A.,Sievers, S.A.,Rome, L.H.,Eisenberg, D. Draft crystal structure of the vault shell at 9-A resolution. Plos Biol., 5:e318-e318, 2007 Cited by 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. PubMed: 18044992DOI: 10.1371/journal.pbio.0050318 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (9 Å) |
Structure validation
Download full validation report
