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- EMDB-19875: Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA O... -

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Basic information

Entry
Database: EMDB / ID: EMD-19875
TitleRefinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
Map data
Sample
  • Complex: Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
KeywordsDNA Origami / Multilayer / Square lattice / 1033 scaffold / DNA / TBA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 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
DepositionMar 18, 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_19875.png

Downloads & links

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Map

FileDownload / File: emd_19875.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0016588437 - 1.6591189
Average (Standard dev.)0.0010845079 (±0.021019474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19875_half_map_1.map
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Half map: #2

Fileemd_19875_half_map_2.map
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Sample components

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Entire : Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA O...

EntireName: Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
Components
  • Complex: Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA

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Supramolecule #1: Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA O...

SupramoleculeName: Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA
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: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
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
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)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 966383
FSC plot (resolution estimation)

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