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- EMDB-11387: 48 helix bundle DNA origami brick -

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Basic information

Entry
Database: EMDB / ID: EMD-11387
Title48 helix bundle DNA origami brick
Map data48 helix bundle DNA origami brick
Sample
  • Complex: 48 helix bundle DNA origami brick
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 Å
AuthorsKube M / Kohler F / Feigl E / Nagel-Yuksel B / Willner EM / Funke JJ / Gerling T / Stommer P / Honemann MN / Martin TG ...Kube M / Kohler F / Feigl E / Nagel-Yuksel B / Willner EM / Funke JJ / Gerling T / Stommer P / Honemann MN / Martin TG / Scheres SHW / Dietz H
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC) Germany
CitationJournal: Nat Commun / Year: 2020
Title: Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W ...Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz /
Abstract: The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is ...The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.
History
DepositionJul 15, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11387.png

Downloads & links

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Map

FileDownload / File: emd_11387.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation48 helix bundle DNA origami brick
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 512 pix.
= 921.6 Å		1.8 Å/pix.
x 512 pix.
= 921.6 Å		1.8 Å/pix.
x 512 pix.
= 921.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.06374877 - 0.19351014
Average (Standard dev.)0.0003279538 (±0.009050218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 921.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z921.600921.600921.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0640.1940.000

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Supplemental data

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Additional map: 2nd quarter of 48 helix bundle DNA origami brick

Fileemd_11387_additional_1.map
Annotation2nd quarter of 48 helix bundle DNA origami brick
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3rd quarter of 48 helix bundle DNA origami brick

Fileemd_11387_additional_2.map
Annotation3rd quarter of 48 helix bundle DNA origami brick
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 4th quarter of 48 helix bundle DNA origami brick

Fileemd_11387_additional_3.map
Annotation4th quarter of 48 helix bundle DNA origami brick
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 1st quarter of 48 helix bundle DNA origami brick

Fileemd_11387_additional_4.map
Annotation1st quarter of 48 helix bundle DNA origami brick
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 48 helix bundle DNA origami brick

EntireName: 48 helix bundle DNA origami brick
Components
  • Complex: 48 helix bundle DNA origami brick

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Supramolecule #1: 48 helix bundle DNA origami brick

SupramoleculeName: 48 helix bundle DNA origami brick / type: complex / ID: 1 / Parent: 0 / Details: DNA Origami
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: 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 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse

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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: 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31931
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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