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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11379 | ||||||||||||
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Title | TwistTower_native-twist | ||||||||||||
![]() | multilayer DNA origami object consisting of 4 parts with crossections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Native crossover spacing corresponding to 10.66bp/turn | ||||||||||||
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Biological species | synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | ||||||||||||
![]() | Kube M / Kohler F / Feigl E / Nagel-Yuksel B / Willner EM / Funke JJ / Gerling T / Stommer P / Honemann MN / Martin TG ...Kube M / Kohler F / Feigl E / Nagel-Yuksel B / Willner EM / Funke JJ / Gerling T / Stommer P / Honemann MN / Martin TG / Scheres SHW / Dietz H | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W ...Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz / ![]() ![]() Abstract: The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is ...The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 206 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.3 KB 28.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() ![]() ![]() ![]() | 11.5 KB 11.5 KB 11.5 KB 11.5 KB 16.7 KB | Display Display Display Display Display | ![]() |
Images | ![]() | 78.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 76.9 MB 6 MB 72.5 MB 72.5 MB 72.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7arvMC ![]() 7areC ![]() 7arqC ![]() 7artC ![]() 7aryC ![]() 7as5C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | multilayer DNA origami object consisting of 4 parts with crossections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Native crossover spacing corresponding to 10.66bp/turn | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Composite map from the four parts, obtained from...
File | emd_11379_additional_1.map | ||||||||||||
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Annotation | Composite map from the four parts, obtained from Relion Multibody Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 2x2 subpart from Multibody Refinement
File | emd_11379_additional_2.map | ||||||||||||
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Annotation | 2x2 subpart from Multibody Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 4x4 subpart from Multibody Refinement
File | emd_11379_additional_3.map | ||||||||||||
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Annotation | 4x4 subpart from Multibody Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 6x6 subpart from Multibody Refinement
File | emd_11379_additional_4.map | ||||||||||||
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Annotation | 6x6 subpart from Multibody Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 8x8 subpart from Multibody Refinement
File | emd_11379_additional_5.map | ||||||||||||
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Annotation | 8x8 subpart from Multibody Refinement | ||||||||||||
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Density Histograms |
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Sample components
-Entire : TwistTower_native-twist
Entire | Name: TwistTower_native-twist |
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Components |
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-Supramolecule #1: TwistTower_native-twist
Supramolecule | Name: TwistTower_native-twist / type: complex / ID: 1 / Parent: 0 Details: multilayer DNA origami object consisting of 4 parts with crossections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Native crossover spacing corresponding to 10.66bp/turn |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
Details | monodisperse, 5 datasets: 1.5uM, 1.0uM, 2.3uM, 2.0uM, 1.75uM |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: CEOS Cs corrector |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 21279 / Average electron dose: 55.0 e/Å2 / Details: magnified pixel size 1.39 A |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus min: 0.2605 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.692 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |