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Yorodumi- PDB-9eoq: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9eoq | ||||||||||||
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Title | Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA | ||||||||||||
Components |
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Keywords | DNA / DNA Origami / Multilayer / Square lattice / 1033 scaffold / TBA | ||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||||||||
Authors | Ali, K. / Georg, K. / Volodymyr, M. / Johanna, G. / Maximilian, N.H. / Lukas, K. / Simone, C. / Hendrik, D. | ||||||||||||
Funding support | European Union, Germany, 3items
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Citation | Journal: Nano Lett / Year: 2024 Title: Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM. Authors: Ali Khoshouei / Georg Kempf / Volodymyr Mykhailiuk / Johanna Mariko Griessing / Maximilian Nicolas Honemann / Lukas Kater / Simone Cavadini / Hendrik Dietz / Abstract: DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular ...DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9eoq.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9eoq.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 9eoq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9eoq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 9eoq_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 9eoq_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 9eoq_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/9eoq ftp://data.pdbj.org/pub/pdb/validation_reports/eo/9eoq | HTTPS FTP |
-Related structure data
Related structure data | 19867MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: DNA chain | Mass: 13034.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 4673.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: synthetic construct (others) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
3D reconstruction | Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 966383 / Symmetry type: POINT |