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Yorodumi- EMDB-43226: DNA origami colloid for self-assembly of tubules: (6,0) monomer -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43226 | |||||||||
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Title | DNA origami colloid for self-assembly of tubules: (6,0) monomer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA origami / synthetic construct / self-assembly / DNA | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 21.89 Å | |||||||||
Authors | Videbaek TE / Rogers WB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43226.map.gz | 116.9 MB | EMDB map data format | |
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Header (meta data) | emd-43226-v30.xml emd-43226.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43226_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_43226.png | 49.7 KB | ||
Masks | emd_43226_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-43226.cif.gz | 4 KB | ||
Others | emd_43226_half_map_1.map.gz emd_43226_half_map_2.map.gz | 98.5 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43226 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43226 | HTTPS FTP |
-Validation report
Summary document | emd_43226_validation.pdf.gz | 951 KB | Display | EMDB validaton report |
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Full document | emd_43226_full_validation.pdf.gz | 950.6 KB | Display | |
Data in XML | emd_43226_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_43226_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43226 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43226 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43226.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.873 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43226_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43226_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43226_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DNA origami colloid for self-assembly of tubules: (6,0) monomer
Entire | Name: DNA origami colloid for self-assembly of tubules: (6,0) monomer |
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Components |
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-Supramolecule #1: DNA origami colloid for self-assembly of tubules: (6,0) monomer
Supramolecule | Name: DNA origami colloid for self-assembly of tubules: (6,0) monomer type: complex / ID: 1 / Parent: 0 |
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Molecular weight | Theoretical: 5.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: C-flat-1.2/1.3 / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 4.0 sec. / Average electron dose: 23.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |