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- EMDB-12016: Programmable icosahedral shell system for virus trapping: DNA-ori... -

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Basic information

Entry
Database: EMDB / ID: EMD-12016
TitleProgrammable icosahedral shell system for virus trapping: DNA-origami octahedron shell
Map data
Sample
  • Complex: DNA-origami octahedron shell
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.2 Å
AuthorsSigl C / Willner EM / Engelen W / Kretzmann JA / Sachenbacher K / Liedl A / Kolbe F / Wilsch F / Aghvami SA / Protzer U ...Sigl C / Willner EM / Engelen W / Kretzmann JA / Sachenbacher K / Liedl A / Kolbe F / Wilsch F / Aghvami SA / Protzer U / Hagan MF / Fraden S / Dietz H
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
CitationJournal: Nat Mater / Year: 2021
Title: Programmable icosahedral shell system for virus trapping.
Authors: Christian Sigl / Elena M Willner / Wouter Engelen / Jessica A Kretzmann / Ken Sachenbacher / Anna Liedl / Fenna Kolbe / Florian Wilsch / S Ali Aghvami / Ulrike Protzer / Michael F Hagan / ...Authors: Christian Sigl / Elena M Willner / Wouter Engelen / Jessica A Kretzmann / Ken Sachenbacher / Anna Liedl / Fenna Kolbe / Florian Wilsch / S Ali Aghvami / Ulrike Protzer / Michael F Hagan / Seth Fraden / Hendrik Dietz /
Abstract: Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not ...Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not available. Here, we describe a programmable icosahedral canvas for the self-assembly of icosahedral shells that have viral trapping and antiviral properties. Programmable triangular building blocks constructed from DNA assemble with high yield into various shell objects with user-defined geometries and apertures. We have created shells with molecular masses ranging from 43 to 925 MDa (8 to 180 subunits) and with internal cavity diameters of up to 280 nm. The shell interior can be functionalized with virus-specific moieties in a modular fashion. We demonstrate this virus-trapping concept by engulfing hepatitis B virus core particles and adeno-associated viruses. We demonstrate the inhibition of hepatitis B virus core interactions with surfaces in vitro and the neutralization of infectious adeno-associated viruses exposed to human cells.
History
DepositionDec 3, 2020-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0221
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0221
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12016.png

Downloads & links

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Map

FileDownload / File: emd_12016.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 560 pix.
= 1276.8 Å		2.28 Å/pix.
x 560 pix.
= 1276.8 Å		2.28 Å/pix.
x 560 pix.
= 1276.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0209 / Movie #1: 0.0221
Minimum - Maximum-0.030792268 - 0.10965792
Average (Standard dev.)0.001198189 (±0.01227472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 1276.7999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.282.282.28
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z1276.8001276.8001276.800
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0310.1100.001

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Supplemental data

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Sample components

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Entire : DNA-origami octahedron shell

EntireName: DNA-origami octahedron shell
Components
  • Complex: DNA-origami octahedron shell

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Supramolecule #1: DNA-origami octahedron shell

SupramoleculeName: DNA-origami octahedron shell / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: 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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

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

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Image processing

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 17.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 3384
Initial angle assignmentType: OTHER
Details: Maximum a posteriori (MAP), Regularized Likelihood Optimization (Relion)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3)
Details: Maximum a posteriori (MAP), Regularized Likelihood Optimization (Relion)
FSC plot (resolution estimation)

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