9EOQ | pdb_00009eoq

Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA

• PDB DOI: https://doi.org/10.2210/pdb9EOQ/pdb
• NAKB: 9EOQ
• EM Map EMD-19867: EMDB EMDataResource

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-03-15 Released: 2024-04-24 
• Deposition Author(s): Ali, K., Georg, K., Volodymyr, M., Johanna, G., Maximilian, N.H., Lukas, K., Simone, C., Hendrik, D.
• Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG), Germanys Excellence Strategy

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM.

Khoshouei, A., Kempf, G., Mykhailiuk, V., Griessing, J.M., Honemann, M.N., Kater, L., Cavadini, S., Dietz, H.

(2024) Nano Lett 24: 5031-5038

• PubMed: 38602296 
• DOI: https://doi.org/10.1021/acs.nanolett.4c00915
• Primary Citation Related Structures: 
  9EOQ


• PubMed 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 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.

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Organizational Affiliation: 
• Laboratory for Biomolecular Nanotechnology, Department of Biosciences, School of Natural Sciences, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany.
Munich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany.
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 17.71 kDa 
• Atom Count: 1,182 
• Modeled Residue Count: 57 
• Deposited Residue Count: 57 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (42-MER)	A	42	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3')	B	15	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Ali, K., Georg, K., Volodymyr, M., Johanna, G., Maximilian, N.H., Lukas, K., Simone, C., Hendrik, D.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101018465
German Research Foundation (DFG)	Germany	--
Germanys Excellence Strategy	Germany	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Database references