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- EMDB-14358: DNA origami rotary ratchet motor -

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Basic information

Entry
Database: EMDB / ID: EMD-14358
TitleDNA origami rotary ratchet motor
Map dataDNA origami rotary ratchet motor
Sample
  • Complex: DNA origami rotary ratchet motor
Biological speciesEscherichia virus M13
Methodsingle particle reconstruction / cryo EM / Resolution: 15.9 Å
AuthorsKube M / Pumm A
Funding supportEuropean Union, Germany, Netherlands, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)724261European Union
German Research Foundation (DFG)SFB863 Germany
Netherlands Organisation for Scientific Research (NWO)no. 019.182EN.03 Netherlands
CitationJournal: Nature / Year: 2022
Title: A DNA origami rotary ratchet motor.
Authors: Anna-Katharina Pumm / Wouter Engelen / Enzo Kopperger / Jonas Isensee / Matthias Vogt / Viktorija Kozina / Massimo Kube / Maximilian N Honemann / Eva Bertosin / Martin Langecker / Ramin ...Authors: Anna-Katharina Pumm / Wouter Engelen / Enzo Kopperger / Jonas Isensee / Matthias Vogt / Viktorija Kozina / Massimo Kube / Maximilian N Honemann / Eva Bertosin / Martin Langecker / Ramin Golestanian / Friedrich C Simmel / Hendrik Dietz /
Abstract: To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. ...To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry. Ratcheting is thought to underpin the function of many natural biological motors, such as the FF-ATPase, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. ) and also in artificial molecular motors created by organic chemical synthesis. DNA nanotechnology has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems, which can adopt different configurations, for example, triggered by strand-displacement reactions or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as FF-ATPase.
History
DepositionFeb 16, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateAug 3, 2022-
Current statusAug 3, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14358.png

Downloads & links

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Map

FileDownload / File: emd_14358.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNA origami rotary ratchet motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.6 Å/pix.
x 256 pix.
= 1177.6 Å		4.6 Å/pix.
x 256 pix.
= 1177.6 Å		4.6 Å/pix.
x 256 pix.
= 1177.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.07519818 - 0.22467515
Average (Standard dev.)0.00014041548 (±0.014053876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 1177.6 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 rotary ratchet motor

EntireName: DNA origami rotary ratchet motor
Components
  • Complex: DNA origami rotary ratchet motor

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Supramolecule #1: DNA origami rotary ratchet motor

SupramoleculeName: DNA origami rotary ratchet motor / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia virus M13
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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-2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / 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: INTEGRATING / Number grids imaged: 1 / Number real images: 1800 / Average exposure time: 3.3 sec. / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 38649
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38649
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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