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- EMDB-19867: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructu... -

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Basic information

Entry
Database: EMDB / ID: EMD-19867
TitleCryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA
Map data
Sample
  • Complex: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA
    • DNA: DNA (42-MER)
    • DNA: DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3')
KeywordsDNA Origami / Multilayer / Square lattice / 1033 scaffold / DNA / TBA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 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 15, 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_19867.png

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Map

FileDownload / File: emd_19867.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.0054948158 - 0.015379195
Average (Standard dev.)-0.00000001787423 (±0.0010173204)
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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Mask #1

Fileemd_19867_msk_1.map
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Additional map: Body2

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Additional map: Body3

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Half map: #2

Fileemd_19867_half_map_1.map
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Half map: #1

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Sample components

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Entire : Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructu...

EntireName: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA
Components
  • Complex: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA
    • DNA: DNA (42-MER)
    • DNA: DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3')

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Supramolecule #1: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructu...

SupramoleculeName: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DNA (42-MER)

MacromoleculeName: DNA (42-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.034333 KDa
SequenceString:
(DA)(DC)(DT)(DT)(DC)(DC)(DA)(DG)(DT)(DC) (DC)(DG)(DT)(DG)(DG)(DT)(DA)(DG)(DG)(DG) (DC)(DA)(DG)(DG)(DT)(DT)(DG)(DG)(DG) (DG)(DT)(DG)(DA)(DC)(DC)(DG)(DC)(DT)(DA) (DT) (DA)(DT)

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Macromolecule #2: DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3')

MacromoleculeName: DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.673059 KDa
SequenceString:
(DA)(DT)(DA)(DT)(DA)(DG)(DC)(DG)(DT)(DG) (DG)(DA)(DA)(DG)(DT)

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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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
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: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 966383
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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