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- EMDB-13567: Stator unit 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-13567
TitleStator unit 3
Map dataComposite map from multibody job of stator unit 3
Sample
  • Complex: stator unit 3
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsBertosin E
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)GA no. 724261 Germany
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Program Germany
German Research Foundation (DFG)SFB863 TPA9 Project ID 111166240 Germany
CitationJournal: Nat Commun / Year: 2021
Title: A nanoscale reciprocating rotary mechanism with coordinated mobility control.
Authors: Eva Bertosin / Christopher M Maffeo / Thomas Drexler / Maximilian N Honemann / Aleksei Aksimentiev / Hendrik Dietz /
Abstract: Biological molecular motors transform chemical energy into mechanical work by coupling cyclic catalytic reactions to large-scale structural transitions. Mechanical deformation can be surprisingly ...Biological molecular motors transform chemical energy into mechanical work by coupling cyclic catalytic reactions to large-scale structural transitions. Mechanical deformation can be surprisingly efficient in realizing such coupling, as demonstrated by the FF ATP synthase. Here, we describe a synthetic molecular mechanism that transforms a rotary motion of an asymmetric camshaft into reciprocating large-scale transitions in a surrounding stator orchestrated by mechanical deformation. We design the mechanism using DNA origami, characterize its structure via cryo-electron microscopy, and examine its dynamic behavior using single-particle fluorescence microscopy and molecular dynamics simulations. While the camshaft can rotate inside the stator by diffusion, the stator's mechanics makes the camshaft pause at preferred orientations. By changing the stator's mechanical stiffness, we accelerate or suppress the Brownian rotation, demonstrating an allosteric coupling between the camshaft and the stator. Our mechanism provides a framework for manufacturing artificial nanomachines that function because of coordinated movements of their components.
History
DepositionSep 8, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0206
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0206
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13567.png

Downloads & links

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Map

FileDownload / File: emd_13567.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map from multibody job of stator unit 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.64 Å/pix.
x 250 pix.
= 1159.5 Å		4.64 Å/pix.
x 250 pix.
= 1159.5 Å		4.64 Å/pix.
x 250 pix.
= 1159.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0206 / Movie #1: 0.0206
Minimum - Maximum-0.01780226 - 0.26544133
Average (Standard dev.)0.0011812551 (±0.011117093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 1159.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.6384.6384.638
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z1159.5001159.5001159.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0180.2650.001

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Supplemental data

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Additional map: Post-processed map of stator unit 3

Fileemd_13567_additional_1.map
AnnotationPost-processed map of stator unit 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : stator unit 3

EntireName: stator unit 3
Components
  • Complex: stator unit 3

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Supramolecule #1: stator unit 3

SupramoleculeName: stator unit 3 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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