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Yorodumi- EMDB-3789: TRIP18SN density map (Design of in vivo self-assembling coiled-co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3789 | |||||||||
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Title | TRIP18SN density map (Design of in vivo self-assembling coiled-coil protein origami) | |||||||||
Map data | TRIP18SN density map (Design of in vivo self-assembling coiled-coil protein origami) | |||||||||
Sample |
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Biological species | Designed protein (others) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.0 Å | |||||||||
Authors | Melero R / Carazo JM | |||||||||
Citation | Journal: Nat Biotechnol / Year: 2017 Title: Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo. Authors: Ajasja Ljubetič / Fabio Lapenta / Helena Gradišar / Igor Drobnak / Jana Aupič / Žiga Strmšek / Duško Lainšček / Iva Hafner-Bratkovič / Andreja Majerle / Nuša Krivec / Mojca ...Authors: Ajasja Ljubetič / Fabio Lapenta / Helena Gradišar / Igor Drobnak / Jana Aupič / Žiga Strmšek / Duško Lainšček / Iva Hafner-Bratkovič / Andreja Majerle / Nuša Krivec / Mojca Benčina / Tomaž Pisanski / Tanja Ćirković Veličković / Adam Round / José María Carazo / Roberto Melero / Roman Jerala / Abstract: Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which ...Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized >20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing >700 amino-acid residues and measuring 11 nm in diameter. Their stability and folding kinetics were similar to those of natural proteins. Solution small-angle X-ray scattering (SAXS), electron microscopy (EM), and biophysical analysis confirmed agreement of the expressed structures with the designs. We also demonstrated self-assembly of a tetrahedral structure in bacteria, mammalian cells, and mice without evidence of inflammation. A semi-automated computational design platform and a toolbox of CC building modules are provided to enable the design of protein cages in any polyhedral shape. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3789.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-3789-v30.xml emd-3789.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_3789.png | 36.2 KB | ||
Filedesc metadata | emd-3789.cif.gz | 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3789 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3789 | HTTPS FTP |
-Validation report
Summary document | emd_3789_validation.pdf.gz | 377.7 KB | Display | EMDB validaton report |
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Full document | emd_3789_full_validation.pdf.gz | 377.3 KB | Display | |
Data in XML | emd_3789_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | emd_3789_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3789 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3789 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3789.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TRIP18SN density map (Design of in vivo self-assembling coiled-coil protein origami) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TRIP18SN
Entire | Name: TRIP18SN |
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Components |
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-Supramolecule #1: TRIP18SN
Supramolecule | Name: TRIP18SN / type: complex / ID: 1 / Parent: 0 Details: Coiled coil single chain protein origami triangular prism composed of soluble dimeric coiled coil segments. |
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Source (natural) | Organism: Designed protein (others) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Staining | Type: NEGATIVE / Material: Uranyl Acetate Details: Samples were applied to glow discharged carbon-coated copper grids, washed quickly with distilled water and negatively stained with 2% (w/v) uranyl acetate. |
-Electron microscopy
Microscope | JEOL 1230 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Xmipp, RELION) / Number images used: 15145 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |