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Yorodumi- EMDB-13884: Broad-spectrum virus-trapping with heparan sulfate-modified DNA o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13884 | |||||||||
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Title | Broad-spectrum virus-trapping with heparan sulfate-modified DNA origami shells: Octahedron shell trapping a HPV | |||||||||
Map data | ||||||||||
Sample |
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 26.5 Å | |||||||||
Authors | Monferrer A / Kretzmann JA / Sigl C / Sapelza P / Liedl A / Dietz H | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: ACS Nano / Year: 2022 Title: Broad-Spectrum Virus Trapping with Heparan Sulfate-Modified DNA Origami Shells. Authors: Alba Monferrer / Jessica A Kretzmann / Christian Sigl / Pia Sapelza / Anna Liedl / Barbara Wittmann / Hendrik Dietz / Abstract: Effective broadband antiviral platforms that can act on existing viruses and viruses yet to emerge are not available, creating a need to explore treatment strategies beyond the trodden paths. Here, ...Effective broadband antiviral platforms that can act on existing viruses and viruses yet to emerge are not available, creating a need to explore treatment strategies beyond the trodden paths. Here, we report virus-encapsulating DNA origami shells that achieve broadband virus trapping properties by exploiting avidity and a widespread background affinity of viruses to heparan sulfate proteoglycans (HSPG). With a calibrated density of heparin and heparan sulfate (HS) derivatives crafted to the interior of DNA origami shells, we could encapsulate adeno, adeno-associated, chikungunya, dengue, human papilloma, noro, polio, rubella, and SARS-CoV-2 viruses or virus-like particles, in one and the same HS-functionalized shell system. Additional virus-type-specific binders were not needed for the trapping. Depending on the relative dimensions of shell to virus particles, multiple virus particles may be trapped per shell, and multiple shells can cover the surface of clusters of virus particles. The steric occlusion provided by the heparan sulfate-coated DNA origami shells can prevent viruses from further interactions with receptors, possibly including those found on cell surfaces. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13884.map.gz | 13.7 MB | EMDB map data format | |
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Header (meta data) | emd-13884-v30.xml emd-13884.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13884_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_13884.png | 43 KB | ||
Others | emd_13884_additional_1.map.gz | 18.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13884 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13884 | HTTPS FTP |
-Validation report
Summary document | emd_13884_validation.pdf.gz | 362.9 KB | Display | EMDB validaton report |
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Full document | emd_13884_full_validation.pdf.gz | 362.4 KB | Display | |
Data in XML | emd_13884_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_13884_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13884 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13884 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13884.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 4.6 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_13884_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T1 shell trapping a chikungunya VLP
Entire | Name: T1 shell trapping a chikungunya VLP |
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Components |
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-Supramolecule #1: T1 shell trapping a chikungunya VLP
Supramolecule | Name: T1 shell trapping a chikungunya VLP / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |