6WR9

Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J32 immobile Holliday junction

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.

Simmons, C.R., MacCulloch, T., Krepl, M., Matthies, M., Buchberger, A., Crawford, I., Sponer, J., Sulc, P., Stephanopoulos, N., Yan, H.

(2022) Nat Commun 13: 3112-3112

  • DOI: https://doi.org/10.1038/s41467-022-30779-6
  • Primary Citation of Related Structures:  
    6WQG, 6WR3, 6WR5, 6WR7, 6WR9, 6WRA, 6WRB, 6WRC, 6WRI, 6WRJ, 6WSN, 6WSO, 6WSP, 6WSQ, 6WSR, 6WSS, 6WST, 6WSU, 6WSV, 6WSW, 6WSX, 6WSY, 6WSZ, 6WT0, 6WT1, 6X8B, 6X8C, 6XDV, 6XDW, 6XDX, 6XDY, 6XDZ, 6XEI, 6XEJ, 6XEK, 6XEL, 6XEM, 6XFC, 6XFD, 6XFE, 6XFF, 6XFG, 6XFW, 6XFX, 6XFY, 6XFZ, 6XG0, 6XGJ, 6XGK, 6XGL

  • PubMed Abstract: 

    • The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials ...

    The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed "fatal," and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

    Organizational Affiliation: 

    School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA. hao.yan@asu.edu.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*AP*GP*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)-3')21synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*GP*TP*CP*T)-3')5synthetic construct
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*G)-3')9synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*GP*TP*CP*TP*GP*C)-3')7synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC
Download Ideal Coordinates CCD File 
F [auth C],
G [auth D]		CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.988α = 90
b = 68.988β = 90
c = 60.793γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1360635
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM104960
National Science Foundation (NSF, United States)United StatesNSF2004250

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references