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- EMDB-3830: Shape-programmable self-limiting hierarchical self-assembly of fi... -

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Basic information

Entry
Database: EMDB / ID: EMD-3830
TitleShape-programmable self-limiting hierarchical self-assembly of finite-size objects through accurate DNA design: V-brick 2.0 for the assembly into 2D finite-size rings
Map dataV-brick 2.0 for the assembly into 2D finite-size rings and higher-order tube-like objects.
Sample
  • Complex: DNA origami
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 31.0 Å
AuthorsDietz H / Wagenbauer KF
CitationJournal: Nature / Year: 2017
Title: Gigadalton-scale shape-programmable DNA assemblies.
Authors: Klaus F Wagenbauer / Christian Sigl / Hendrik Dietz /
Abstract: Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures ...Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.
History
DepositionJul 29, 2017-
Header (metadata) releaseAug 30, 2017-
Map releaseDec 20, 2017-
UpdateDec 20, 2017-
Current statusDec 20, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3830.png

Downloads & links

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Map

FileDownload / File: emd_3830.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationV-brick 2.0 for the assembly into 2D finite-size rings and higher-order tube-like objects.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.32 Å/pix.
x 400 pix.
= 927.6 Å		2.32 Å/pix.
x 400 pix.
= 927.6 Å		2.32 Å/pix.
x 400 pix.
= 927.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.319 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.06287589 - 0.23503608
Average (Standard dev.)0.0047254134 (±0.021000955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 927.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.3192.3192.319
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z927.600927.600927.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0630.2350.005

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Supplemental data

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Sample components

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Entire : DNA origami

EntireName: DNA origami
Components
  • Complex: DNA origami

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Supramolecule #1: DNA origami

SupramoleculeName: DNA origami / type: complex / ID: 1 / Parent: 0 / Details: Includes two M13-derived genomic scaffold chains
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)
Molecular weightTheoretical: 11 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: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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: 20.0 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: 31.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 4200
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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