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- EMDB-17600: DNA-origami turbine with left-handed chirality -

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Basic information

Entry
Database: EMDB / ID: EMD-17600
TitleDNA-origami turbine with left-handed chirality
Map dataDNA-origami turbine with left-handed chirality
Sample
  • Complex: DNA Origami
    • Complex: scaffold DNA single strand
    • Complex: staple oligonucleotides
KeywordsDNA-origami / DNA nanoturbine / nanorobotics / nanomachine / rotary motor / hydrodynamic flows / DNA
Biological speciesInovirus M13 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsShi X / Pumm A-K / Maffeo C / Kohler F / Feigl E / Zhao W / Verschueren D / Golestanian R / Aksimentiev A / Dietz H / Dekker C
Funding supportEuropean Union, Netherlands, Germany, United States, 7 items
OrganizationGrant numberCountry
European Research Council (ERC)883684European Union
Netherlands Organisation for Scientific Research (NWO)BaSyC Netherlands
Other governmentNanoFront Netherlands
European Research Council (ERC)724261European Union
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Program Germany
German Research Foundation (DFG)SFB863 111166240 TPA9 Germany
National Science Foundation (NSF, United States)DMR-1827346 United States
CitationJournal: To Be Published
Title: A nanopore-powered DNA turbine
Authors: Shi X / Pumm A-K / Maffeo C / Kohler F / Feigl E / Zhao W / Verschueren D / Golestanian R / Aksimentiev A / Dietz H / Dekker C
History
DepositionJun 11, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17600.png

Downloads & links

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Map

FileDownload / File: emd_17600.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNA-origami turbine with left-handed chirality
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 400 pix.
= 912. Å		2.28 Å/pix.
x 400 pix.
= 912. Å		2.28 Å/pix.
x 400 pix.
= 912. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.058
Minimum - Maximum-0.046107173 - 0.19006783
Average (Standard dev.)0.00026548727 (±0.0050655017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 912.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: DNA-origami turbine with left-handed chirality - unfiltered half...

Fileemd_17600_half_map_1.map
AnnotationDNA-origami turbine with left-handed chirality - unfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DNA-origami turbine with left-handed chirality - unfiltered half...

Fileemd_17600_half_map_2.map
AnnotationDNA-origami turbine with left-handed chirality - unfiltered 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 Origami

EntireName: DNA Origami
Components
  • Complex: DNA Origami
    • Complex: scaffold DNA single strand
    • Complex: staple oligonucleotides

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Supramolecule #1: DNA Origami

SupramoleculeName: DNA Origami / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: scaffold DNA single strand

SupramoleculeName: scaffold DNA single strand / type: complex / ID: 2 / Parent: 1 / Details: m13mp18-derived, 8064 bases
Source (natural)Organism: Inovirus M13

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Supramolecule #3: staple oligonucleotides

SupramoleculeName: staple oligonucleotides / type: complex / ID: 3 / Parent: 1 / Details: chemically synthesized
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: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 40 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 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: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE / Details: De novo 3D Initial Model created in Relion
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 71992
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0beta) / Details: Regularized Likelihood Optimization (Relion)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0beta) / Details: Regularized Likelihood Optimization (Relion)
FSC plot (resolution estimation)

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