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- EMDB-16238: Triangle-1-version-3 for DNA ORIGAMI TRAPS FOR LARGE VIRUSES -

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Basic information

Entry
Database: EMDB / ID: EMD-16238
TitleTriangle-1-version-3 for DNA ORIGAMI TRAPS FOR LARGE VIRUSES
Map dataDNAOrigamiVirusTrap_T1v3
Sample
  • Complex: DNA Origami
    • Complex: scaffold DNA single-strand
    • Complex: staple ssDNA oligonucleotides
KeywordsDNA origami / high-order assemblies / antivirals / virus trapping / DNA
Biological speciesInovirus M13 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsMonferrer A / Kohler F / Sigl C / Schachtner M / Peterhoff D / Asbach B / Wagner R / Dietz H
Funding supportEuropean Union, Germany, 4 items
OrganizationGrant numberCountry
European Union (EU)899619European Union
Marie Sklodowska-Curie Actions, FragNET ITN7657039European Union
German Research Foundation (DFG)DI1500/5 Germany
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Program Germany
CitationJournal: Cell Rep Phys Sci / Year: 2023
Title: DNA origami traps for large viruses
Authors: Monferrer A / Kohler F / Sigl C / Schachtner M / Peterhoff D / Asbach B / Wagner R / Dietz H
History
DepositionNov 29, 2022-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16238.png

Downloads & links

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Map

FileDownload / File: emd_16238.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNAOrigamiVirusTrap_T1v3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.56 Å/pix.
x 400 pix.
= 1824. Å		4.56 Å/pix.
x 400 pix.
= 1824. Å		4.56 Å/pix.
x 400 pix.
= 1824. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.06091748 - 0.29551739
Average (Standard dev.)0.00028647954 (±0.0061822184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 1824.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: DNAOrigamiVirusTrap T1v3

Fileemd_16238_half_map_1.map
AnnotationDNAOrigamiVirusTrap_T1v3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DNAOrigamiVirusTrap T1v3

Fileemd_16238_half_map_2.map
AnnotationDNAOrigamiVirusTrap_T1v3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA Origami

EntireName: DNA Origami
Components
  • Complex: DNA Origami
    • Complex: scaffold DNA single-strand
    • Complex: staple ssDNA oligonucleotides

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Supramolecule #1: DNA Origami

SupramoleculeName: DNA Origami / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: scaffold DNA single-strand

SupramoleculeName: scaffold DNA single-strand / type: complex / ID: 2 / Parent: 1 / Details: 8064 bases
Source (natural)Organism: Inovirus M13

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Supramolecule #3: staple ssDNA oligonucleotides

SupramoleculeName: staple ssDNA oligonucleotides / type: complex / ID: 3 / Parent: 1 / Details: chemically synthesized
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
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / 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: 60.0 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 / Nominal defocus max: 3.819074 µm / Nominal defocus min: 1.5 µm
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

Startup modelType of model: INSILICO MODEL / In silico model: De novo 3D Initial Model created in Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 29197
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: Regularized Likelihood Optimization (Relion)
Final angle assignmentType: OTHER / Software - Name: RELION / Details: Regularized Likelihood Optimization (Relion)
FSC plot (resolution estimation)

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