4V5X

The cryo-EM structure of a 3D DNA-origami object


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 3.1 of the entry. See complete history


Literature

Cryo-Em Structure of a 3D DNA-Origami Object.

Bai, X.Martin, T.G.Scheres, S.H.W.Dietz, H.

(2012) Proc Natl Acad Sci U S A 109: 20012

  • DOI: https://doi.org/10.1073/pnas.1215713109
  • Primary Citation of Related Structures:  
    4V5X

  • PubMed Abstract: 

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback.


  • Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.


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SCAFFOLD STRAND,SCAFFOLD STRANDA [auth AA]7,249Inovirus M13
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STAPLE STRANDID [auth C3]48synthetic construct
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STAPLE STRANDLD [auth C6]48synthetic construct
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STAPLE STRANDMD [auth C7]52synthetic construct
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MoleculeChains LengthOrganismImage
STAPLE STRANDOD [auth CB]54synthetic construct
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MoleculeChains LengthOrganismImage
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MoleculeChains LengthOrganismImage
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MoleculeChains LengthOrganismImage
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MoleculeChains LengthOrganismImage
STAPLE STRANDME [auth CZ]48synthetic construct
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MoleculeChains LengthOrganismImage
STAPLE STRANDWE [auth Cq]40synthetic construct
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Entity ID: 154
MoleculeChains LengthOrganismImage
STAPLE STRANDXE [auth Cr]46synthetic construct
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Entity ID: 156
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Entity ID: 157
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Entity ID: 158
MoleculeChains LengthOrganismImage
STAPLE STRANDBF [auth Cv]46synthetic construct
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Entity ID: 159
MoleculeChains LengthOrganismImage
STAPLE STRANDCF [auth Cw]54synthetic construct
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Entity ID: 160
MoleculeChains LengthOrganismImage
STAPLE STRANDDF [auth Cx]46synthetic construct
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Entity ID: 161
MoleculeChains LengthOrganismImage
STAPLE STRANDEF [auth Cy]66synthetic construct
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Entity ID: 162
MoleculeChains LengthOrganismImage
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report

Currently 4V5X does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-25
    Changes: Other
  • Version 2.0: 2017-08-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 3.0: 2019-07-31
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 3.1: 2019-12-11
    Changes: Other