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- EMDB-43227: DNA origami colloid for self-assembly of tubules: (10,0) monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-43227
TitleDNA origami colloid for self-assembly of tubules: (10,0) monomer
Map dataPrimary map of the (10,0) monomer.
Sample
  • Complex: DNA origami colloid for self-assembly of tubules: (10,0) monomer
KeywordsDNA origami / synthetic construct / self-assembly / DNA
Methodsingle particle reconstruction / cryo EM / Resolution: 20.88 Å
AuthorsVidebaek TE / Rogers WB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2011846 United States
CitationJournal: Sci Adv / Year: 2024
Title: Economical routes to size-specific assembly of self-closing structures.
Authors: Thomas E Videbæk / Daichi Hayakawa / Gregory M Grason / Michael F Hagan / Seth Fraden / W Benjamin Rogers /
Abstract: Programmable self-assembly has seen an explosion in the diversity of synthetic crystalline materials, but developing strategies that target "self-limiting" assemblies has remained a challenge. Among ...Programmable self-assembly has seen an explosion in the diversity of synthetic crystalline materials, but developing strategies that target "self-limiting" assemblies has remained a challenge. Among these, self-closing structures, in which the local curvature defines the finite global size, are prone to polymorphism due to thermal bending fluctuations, a problem that worsens with increasing target size. Here, we show that assembly complexity can be used to eliminate this source of polymorphism in the assembly of tubules. Using many distinct components, we prune the local density of off-target geometries, increasing the selectivity of the tubule width and helicity to nearly 100%. We further show that by reducing the design constraints to target either the pitch or the width alone, fewer components are needed to reach complete selectivity. Combining experiments with theory, we reveal an economical limit, which determines the minimum number of components required to create arbitrary assembly sizes with full selectivity.
History
DepositionDec 29, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43227.png

Downloads & links

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Map

FileDownload / File: emd_43227.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map of the (10,0) monomer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.02 Å/pix.
x 360 pix.
= 728.28 Å		2.02 Å/pix.
x 360 pix.
= 728.28 Å		2.02 Å/pix.
x 360 pix.
= 728.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.023 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.018350853 - 0.05404278
Average (Standard dev.)0.00046717282 (±0.006223483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 728.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43227_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the structure.

Fileemd_43227_half_map_1.map
AnnotationHalf-map of the structure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the structure.

Fileemd_43227_half_map_2.map
AnnotationHalf-map of the structure.
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 colloid for self-assembly of tubules: (10,0) monomer

EntireName: DNA origami colloid for self-assembly of tubules: (10,0) monomer
Components
  • Complex: DNA origami colloid for self-assembly of tubules: (10,0) monomer

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Supramolecule #1: DNA origami colloid for self-assembly of tubules: (10,0) monomer

SupramoleculeName: DNA origami colloid for self-assembly of tubules: (10,0) monomer
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 5.2 MDa

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 775 / Average exposure time: 1.4 sec. / Average electron dose: 69.8 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3808 / Details: Manual selection
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 2153
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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