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- EMDB-26325: METIS hexagonal wireframe DNA origami with 106bp edge length_no mesh -

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Basic information

Entry
Database: EMDB / ID: EMD-26325
TitleMETIS hexagonal wireframe DNA origami with 106bp edge length_no mesh
Map data
Sample
  • Complex: METIS hexagonal wireframe DNA origami with 106bp edge length_no mesh
Biological speciesEscherichia virus M13
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsLi S / Wang X / Zhang K / Chiu W / Bathe M
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CBET-1729397 United States
National Science Foundation (NSF, United States)CCF-1956054 United States
Office of Naval Research (ONR)N00014-21-1-4013 United States
Office of Naval Research (ONR)N00014-20-1-2084 United States
CitationJournal: Sci Adv / Year: 2022
Title: Planar 2D wireframe DNA origami.
Authors: Xiao Wang / Shanshan Li / Hyungmin Jun / Torsten John / Kaiming Zhang / Hannah Fowler / Jonathan P K Doye / Wah Chiu / Mark Bathe /
Abstract: Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in ...Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo-electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.
History
DepositionFeb 27, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJun 29, 2022-
Current statusJun 29, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26325.png

Downloads & links

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Map

FileDownload / File: emd_26325.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 300 pix.
= 630. Å		2.1 Å/pix.
x 300 pix.
= 630. Å		2.1 Å/pix.
x 300 pix.
= 630. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.1849142 - 2.9024756
Average (Standard dev.)0.0018060466 (±0.08996099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 630.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : METIS hexagonal wireframe DNA origami with 106bp edge length_no mesh

EntireName: METIS hexagonal wireframe DNA origami with 106bp edge length_no mesh
Components
  • Complex: METIS hexagonal wireframe DNA origami with 106bp edge length_no mesh

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Supramolecule #1: METIS hexagonal wireframe DNA origami with 106bp edge length_no mesh

SupramoleculeName: METIS hexagonal wireframe DNA origami with 106bp edge length_no mesh
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia virus M13

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21809
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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