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- EMDB-19129: A DNA Robotic Switch with Regulated Autonomous Display of Cytotox... -

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Basic information

Entry
Database: EMDB / ID: EMD-19129
TitleA DNA Robotic Switch with Regulated Autonomous Display of Cytotoxic Ligand Nanopatterns
Map dataFrom cryoSPARC 3DFlex reconstruct job
Sample
  • Complex: DNA origami
    • Complex: ssDNA staples
    • Complex: ssDNA scaffold
KeywordsDNA / DNA origami / Lgand nanopattern / pH sensitive switch / Solid tumor / Death receptor clustering
Biological speciessynthetic construct (others) / Phage M13mp18 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsWang Y / Berzina I / Hogberg B
Funding support Sweden, European Union, Finland, 6 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2017.0114 Sweden
Knut and Alice Wallenberg FoundationKAW 2017.0276) Sweden
European Research Council (ERC)Cell Track GA No. 724872European Union
Swedish Research Council2019-01474 Sweden
Swedish Research Council2023-00289 Sweden
Academy of Finland341908 Finland
CitationJournal: Nat Nanotechnol / Year: 2024
Title: A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns.
Authors: Wang Y / Baars I / Berzina I / Rocamonde-Lago I / Shen B / Yang Y / Lolaico M / Waldvogel J / Smyrlaki I / Zhu K / Harris RA / Hogberg B
History
DepositionDec 13, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19129.png

Downloads & links

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Map

FileDownload / File: emd_19129.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFrom cryoSPARC 3DFlex reconstruct job
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.023316177 - 0.07724496
Average (Standard dev.)0.0013319443 (±0.0054964432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 704.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DNA origami

EntireName: DNA origami
Components
  • Complex: DNA origami
    • Complex: ssDNA staples
    • Complex: ssDNA scaffold

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Supramolecule #1: DNA origami

SupramoleculeName: DNA origami / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)

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Supramolecule #2: ssDNA staples

SupramoleculeName: ssDNA staples / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: ssDNA scaffold

SupramoleculeName: ssDNA scaffold / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Phage M13mp18 (virus)

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: 5 mM MgCl2, 5 mM NaCl, 5 mM TRIS, and 1 mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 10 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 6652 / #0 - Average exposure time: 4.4 sec. / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 5195 / #1 - Average exposure time: 6.0 sec. / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
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

Image recording ID1
Startup modelType of model: OTHER / Details: Ab initio map
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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