5KEK

Structure Determination of a Self-Assembling DNA Crystal

  • Classification: DNA
  • Organism(s): Endothia gyrosa
  • Mutation(s): No 

  • Deposited: 2016-06-09 Released: 2016-08-10 
  • Deposition Author(s): Simmons, C.R., Birktoft, J.J., Seeman, N.C., Yan, H.
  • Funding Organization(s): Department of Energy (DOE, United States), National Science Foundation (NSF, United States), Army Research Office, Office of Naval Research, Gordon and Betty Moore Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Construction and Structure Determination of a Three-Dimensional DNA Crystal.

Simmons, C.R., Zhang, F., Birktoft, J.J., Qi, X., Han, D., Liu, Y., Sha, R., Abdallah, H.O., Hernandez, C., Ohayon, Y.P., Seeman, N.C., Yan, H.

(2016) J Am Chem Soc 138: 10047-10054

  • DOI: https://doi.org/10.1021/jacs.6b06508
  • Primary Citation of Related Structures:  
    5KEK, 5KEO

  • PubMed Abstract: 

    • Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices ...

    Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif we used employs a five-nucleotide repeating sequence that weaves through a series of two-turn DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in turn assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for the design of new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays differ by the use of four or six repeats of the five-nucleotide units in the repeating but statistically disordered central strand. In addition, we report a 2D rhombuslike array formed from similar components.

    Organizational Affiliation: 

    Department of Chemistry, New York University , New York, New York 10003, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')A21Endothia gyrosa
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*GP*TP*CP*A)-3')B5Endothia gyrosa
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3')C9Endothia gyrosa
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')D7Endothia gyrosa
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC
Download Ideal Coordinates CCD File 
E [auth C],
F [auth D]		CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.926α = 90
b = 67.926β = 90
c = 59.262γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0007991
National Science Foundation (NSF, United States)United StatesCCF-1526650
National Science Foundation (NSF, United States)United StatesEFRI-1332411
National Science Foundation (NSF, United States)United StatesCCF-1526650
Army Research OfficeUnited StatesW911NF-11-1-0024
Office of Naval ResearchUnited StatesN000141110729
Department of Energy (DOE, United States)United StatesDE-SC0007991
Gordon and Betty Moore FoundationUnited StatesGBMF3849

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence