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- EMDB-16219: Triple-stranded DNA as a structural element in DNA origami large ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16219
TitleTriple-stranded DNA as a structural element in DNA origami large cuboid with TFO object
Map dataDNA origami object with triple - stranded DNA segment
Sample
  • Complex: DNA Nanostructure
    • Complex: Scaffold DNA single-strand
    • Complex: Staple oligonucleotides
KeywordsDNA Origami / Triplex forming Oligo / Triplex / TFO / large cuboid / large cuboid with TFO / DNA
Biological speciessynthetic construct (others) / Phage M13mp18 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.08 Å
AuthorsSachenbacher K / Khoshouei A / Honemann MN / Engelen W / Feigl E / Dietz H
Funding supportEuropean Union, Germany, Netherlands, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)101018465European Union
German Research Foundation (DFG) Germany
Netherlands Organisation for Scientific Research (NWO)019.182EN.037 Netherlands
European Union (EU)899619European Union
CitationJournal: Acs Nano / Year: 2023
Title: Triple-Stranded DNA As a Structural Element in DNA Origami
Authors: Sachenbacher K / Khoshouei A / Honemann MN / Engelen W / Feigl E / Dietz H
History
DepositionNov 23, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16219.png

Downloads & links

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Map

FileDownload / File: emd_16219.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNA origami object with triple - stranded DNA segment
Voxel sizeX=Y=Z: 2.1 Å
Density
Contour LevelBy AUTHOR: 0.0404
Minimum - Maximum-0.053635225 - 0.20306112
Average (Standard dev.)0.002786783 (±0.016143413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: DNA origami object with triple - stranded DNA segment / half map 2

Fileemd_16219_half_map_1.map
AnnotationDNA origami object with triple - stranded DNA segment / half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DNA origami object with triple - stranded DNA segment / half map 1

Fileemd_16219_half_map_2.map
AnnotationDNA origami object with triple - stranded DNA segment / half map 1
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 Nanostructure

EntireName: DNA Nanostructure
Components
  • Complex: DNA Nanostructure
    • Complex: Scaffold DNA single-strand
    • Complex: Staple oligonucleotides

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Supramolecule #1: DNA Nanostructure

SupramoleculeName: DNA Nanostructure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #2: Scaffold DNA single-strand

SupramoleculeName: Scaffold DNA single-strand / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Phage M13mp18 (virus)

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Supramolecule #3: Staple oligonucleotides

SupramoleculeName: Staple oligonucleotides / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
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: 5 / Details: 5 mM MES, 5mM NaCl and 5 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000
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 generated initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110804
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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