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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13478 | |||||||||
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Title | Vault structure in primmed conformation | |||||||||
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![]() | Transport / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding ...protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Guerra P / Gonzalez-Alamos M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Symmetry disruption commits vault particles to disassembly. Authors: Pablo Guerra / María González-Alamos / Aida Llauró / Arnau Casañas / Jordi Querol-Audí / Pedro J de Pablo / Núria Verdaguer / ![]() Abstract: Vaults are ubiquitous ribonucleoprotein particles involved in a diversity of cellular processes, with promising applications as nanodevices for delivery of multiple cargos. The vault shell is ...Vaults are ubiquitous ribonucleoprotein particles involved in a diversity of cellular processes, with promising applications as nanodevices for delivery of multiple cargos. The vault shell is assembled by the symmetrical association of multiple copies of the major vault protein that, initially, generates half vaults. The pairwise, anti-parallel association of two half vaults produces whole vaults. Here, using a combination of vault recombinant reconstitution and structural techniques, we characterized the molecular determinants for the vault opening process. This process commences with a relaxation of the vault waist, causing the expansion of the inner cavity. Then, local disengagement of amino-terminal domains at the vault midsection seeds a conformational change that leads to the aperture, facilitating access to the inner cavity where cargo is hosted. These results inform a hitherto uncharacterized step of the vault cycle and will aid current engineering efforts leveraging vault for tailored cargo delivery. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.8 KB 11.8 KB | Display Display | ![]() |
Images | ![]() | 69.8 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pkrMC ![]() 7pkyC ![]() 7pkzC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.69 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : major vault protein from Rattus norvegicus
Entire | Name: major vault protein from Rattus norvegicus |
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Components |
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-Supramolecule #1: major vault protein from Rattus norvegicus
Supramolecule | Name: major vault protein from Rattus norvegicus / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Major vault protein
Macromolecule | Name: Major vault protein / type: protein_or_peptide / ID: 1 / Number of copies: 78 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 95.920109 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MATEEAIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPVRM VTVPPRHYCI VANPVSRDTQ SSVLFDITGQ VRLRHADQE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKNGDKVMA GDEWLFEGPG TYIPQKEVEV V EIIQATVI ...String: MATEEAIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPVRM VTVPPRHYCI VANPVSRDTQ SSVLFDITGQ VRLRHADQE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKNGDKVMA GDEWLFEGPG TYIPQKEVEV V EIIQATVI KQNQALRLRA RKECFDREGK GRVTGEEWLV RSVGAYLPAV FEEVLDLVDA VILTEKTALH LRALQNFRDL RG VLHRTGE EWLVTVQDTE AHVPDVYEEV LGVVPITTLG PRHYCVILDP MGPDGKNQLG QKRVVKGEKS FFLQPGERLE RGI QDVYVL SEQQGLLLKA LQPLEEGESE EKVSHQAGDC WLIRGPLEYV PSAKVEVVEE RQAIPLDQNE GIYVQDVKTG KVRA VIGST YMLTQDEVLW EKELPSGVEE LLNLGHDPLA DRGQKGTAKP LQPSAPRNKT RVVSYRVPHN AAVQVYDYRA KRARV VFGP ELVTLDPEEQ FTVLSLSAGR PKRPHARRAL CLLLGPDFFT DVITIETADH ARLQLQLAYN WHFELKNRND PAEAAK LFS VPDFVGDACK AIASRVRGAV ASVTFDDFHK NSARIIRMAV FGFEMSEDTG PDGTLLPKAR DQAVFPQNGL VVSSVDV QS VEPVDQRTRD ALQRSVQLAI EITTNSQEAA AKHEAQRLEQ EARGRLERQK ILDQSEAEKA RKELLELEAM SMAVESTG N AKAEAESRAE AARIEGEGSV LQAKLKAQAL AIETEAELER VKKVREMELI YARAQLELEV SKAQQLANVE AKKFKEMTE ALGPGTIRDL AVAGPEMQVK LLQSLGLKST LITDGSSPIN LFSTAFGLLG LGSDGQPPAQ K UniProtKB: Major vault protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9793 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |