8FI0

Structure of Lettuce aptamer bound to DFAME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Intricate 3D architecture of a DNA mimic of GFP.

Passalacqua, L.F.M.Banco, M.T.Moon, J.D.Li, X.Jaffrey, S.R.Ferre-D'Amare, A.R.

(2023) Nature 618: 1078-1084

  • DOI: https://doi.org/10.1038/s41586-023-06229-8
  • Primary Citation of Related Structures:  
    8FHV, 8FHX, 8FHZ, 8FI0, 8FI1, 8FI2, 8FI7, 8FI8

  • PubMed Abstract: 

    Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures 1-3 . By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates 4 conditional fluorophores derived from GFP. To extend previous structural studies 5,6 of fluorogenic RNAs, GFP and other fluorescent proteins 7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen 8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.


  • Organizational Affiliation

    Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Lettuce DNA aptamer53synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X5R (Subject of Investigation/LOI)
Query on X5R

Download Ideal Coordinates CCD File 
H [auth A]methyl (2E)-3-{(4Z)-4-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-1-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl}prop-2-enoate
C15 H12 F2 N2 O4
LXQQJPJEYBZZSO-ZDVGJPJSSA-N
K
Query on K

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.876α = 90
b = 43.022β = 90
c = 119.622γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection