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- EMDB-48634: DNA-origami colloid for self-assembly of tubules: (10,0) monomer,... -

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Basic information

Entry
Database: EMDB / ID: EMD-48634
TitleDNA-origami colloid for self-assembly of tubules: (10,0) monomer, bound pair from side 2 interaction
Map dataPrimary electron density map.
Sample
  • Complex: DNA-origami colloid for self-assembly of tubules: (10,0) monomer, bound pair from side 2 interaction
KeywordsDNA origami / synthetic construct / DNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 27.58 Å
AuthorsVidebaek TE / Rogers WB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2011846 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Measuring multisubunit mechanics of geometrically programmed colloidal assemblies via cryo-EM multi-body refinement.
Authors: Thomas E Videbæk / Daichi Hayakawa / Michael F Hagan / Gregory M Grason / Seth Fraden / W Benjamin Rogers /
Abstract: Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more ...Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional assemblies necessitates going beyond the design of the structure itself, to the measurement and control of the local flexibility of the intersubunit connections and its impact on the collective mechanics of the entire assembly. In this study, we demonstrate a method to infer the mechanical properties of multisubunit assemblies using cryogenic electron microscopy (cryo-EM) and RELION's multi-body refinement. Specifically, we analyze the fluctuations of pairs of DNA-origami subunits that self-assemble into tubules. By measuring the fluctuations of dimers using cryo-EM, we extract mechanical properties such as the bending modulus and interparticle spring constant. These properties are then applied to elastic models to predict assembly outcomes, which align well with experimental observations. This approach not only provides a deeper understanding of nanoparticle mechanics but also opens pathways to refining subunit designs to achieve precise assembly behavior. This methodology could have broader applications in the study of nanomaterials, including protein assemblies, where understanding the interplay of mechanical properties and subunit geometry is essential for controlling complex self-assembled structures.
History
DepositionJan 14, 2025-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48634.png

Downloads & links

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Map

FileDownload / File: emd_48634.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary electron density map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.9 Å/pix.
x 200 pix.
= 1379.04 Å		6.9 Å/pix.
x 200 pix.
= 1379.04 Å		6.9 Å/pix.
x 200 pix.
= 1379.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.8952 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.07736234 - 0.23933652
Average (Standard dev.)0.0004918022 (±0.01744369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 1379.0399 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Second half map of the structure.

Fileemd_48634_half_map_1.map
AnnotationSecond half map of the structure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half map of the structure

Fileemd_48634_half_map_2.map
AnnotationFirst half 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, bound pair from side 2 interaction
Components
  • Complex: DNA-origami colloid for self-assembly of tubules: (10,0) monomer, bound pair from side 2 interaction

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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, bound pair from side 2 interaction
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes
Molecular weightTheoretical: 10.4 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: 7
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: OTHER / Number real images: 584 / Average exposure time: 4.0 sec. / Average electron dose: 22.0 e/Å2 / Details: GATAN Oneview CMOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.8 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 2.2 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4122
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 27.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 3962
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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