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- EMDB-19767: Structure of a 2873 Scaffold Base DNA Origami V1 -

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Basic information

Entry
Database: EMDB / ID: EMD-19767
TitleStructure of a 2873 Scaffold Base DNA Origami V1
Map data
Sample
  • Complex: Structure of a 2873 Scaffold Base DNA Origami V1
KeywordsDNA Origami / Multilayer / Square lattice / 2873 scaffold / DNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsAli K / Georg K / Volodymyr M / Johanna G / Maximilian NH / Lukas K / Simone C / Hendrik D
Funding supportEuropean Union, Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)101018465European Union
German Research Foundation (DFG) Germany
Germanys Excellence Strategy Germany
CitationJournal: Nano Lett / Year: 2024
Title: Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM.
Authors: Ali Khoshouei / Georg Kempf / Volodymyr Mykhailiuk / Johanna Mariko Griessing / Maximilian Nicolas Honemann / Lukas Kater / Simone Cavadini / Hendrik Dietz /
Abstract: DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular ...DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications.
History
DepositionFeb 29, 2024-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19767.png

Downloads & links

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Map

FileDownload / File: emd_19767.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 270 pix.
= 378. Å		1.4 Å/pix.
x 270 pix.
= 378. Å		1.4 Å/pix.
x 270 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.22430636 - 0.4767326
Average (Standard dev.)0.005957618 (±0.027132118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19767_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19767_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of a 2873 Scaffold Base DNA Origami V1

EntireName: Structure of a 2873 Scaffold Base DNA Origami V1
Components
  • Complex: Structure of a 2873 Scaffold Base DNA Origami V1

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Supramolecule #1: Structure of a 2873 Scaffold Base DNA Origami V1

SupramoleculeName: Structure of a 2873 Scaffold Base DNA Origami V1 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / 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) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio model generated in Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140317
Initial angle assignmentType: OTHER / Software - Name: RELION
Details: Maximum a posteriori (MAP), REgularized LIkelihood OptimizatioN (Relion)
Final angle assignmentType: OTHER / Software - Name: RELION
Details: Maximum a posteriori (MAP), REgularized LIkelihood OptimizatioN (Relion)
FSC plot (resolution estimation)

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