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- EMDB-13883: Broad-spectrum virus-trapping with heparan sulfate-modified DNA o... -

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Basic information

Entry
Database: EMDB / ID: EMD-13883
TitleBroad-spectrum virus-trapping with heparan sulfate-modified DNA origami shells: T1 shell trapping a chikungunya VLP
Map dataT=1 shell trapping chikungunya
Sample
  • Complex: T1 shell trapping a chikungunya VLP
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 36.3 Å
AuthorsMonferrer A / Kretzmann JA / Sigl C / Sapelza P / Liedl A / Dietz H
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: 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
DepositionNov 18, 2021-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13883.png

Downloads & links

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Map

FileDownload / File: emd_13883.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT=1 shell trapping chikungunya
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.8 Å/pix.
x 300 pix.
= 1740. Å		5.8 Å/pix.
x 300 pix.
= 1740. Å		5.8 Å/pix.
x 300 pix.
= 1740. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0339
Minimum - Maximum-0.12809037 - 0.18709844
Average (Standard dev.)0.0032024058 (±0.016888538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 1740.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : T1 shell trapping a chikungunya VLP

EntireName: T1 shell trapping a chikungunya VLP
Components
  • Complex: T1 shell trapping a chikungunya VLP

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Supramolecule #1: T1 shell trapping a chikungunya VLP

SupramoleculeName: T1 shell trapping a chikungunya VLP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Details: maximum a posteriori (MAP), Regularized Likelihood OptimizatioN (Relion)
Final angle assignmentType: OTHER
Details: maximum a posteriori (MAP), Regularized Likelihood OptimizatioN (Relion)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 36.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1259
FSC plot (resolution estimation)

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