6M4T

U shaped head to head four-way junction in d(TTCTGCTGCTGAA) sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report



Literature

Structural Basis for Targeting T:T Mismatch with Triaminotriazine-Acridine Conjugate Induces a U-Shaped Head-to-Head Four-Way Junction in CTG Repeat DNA.

Chien, C.M.Wu, P.C.Satange, R.Chang, C.C.Lai, Z.L.Hagler, L.D.Zimmerman, S.C.Hou, M.H.

(2020) J Am Chem Soc 142: 11165-11172

  • DOI: 10.1021/jacs.0c03591
  • Primary Citation of Related Structures:  
    6M4T, 6M5J

  • PubMed Abstract: 
  • The potent DNA-binding compound triaminotriazine-acridine conjugate (Z1) functions by targeting T:T mismatches in CTG trinucleotide repeats that are responsible for causing neurological diseases such as myotonic dystrophy type 1, but its binding mech ...

    The potent DNA-binding compound triaminotriazine-acridine conjugate (Z1) functions by targeting T:T mismatches in CTG trinucleotide repeats that are responsible for causing neurological diseases such as myotonic dystrophy type 1, but its binding mechanism remains unclear. We solved a crystal structure of Z1 in a complex with DNA containing three consecutive CTG repeats with three T:T mismatches. Crystallographic studies revealed that direct intercalation of two Z1 molecules at both ends of the CTG repeat induces thymine base flipping and DNA backbone deformation to form a four-way junction. The core of the complex unexpectedly adopts a U-shaped head-to-head topology to form a crossover of each chain at the junction site. The crossover junction is held together by two stacked G:C pairs at the central core that rotate with respect to each other in an X-shape to form two nonplanar minor-groove-aligned G·C·G·C tetrads. Two stacked G:C pairs on both sides of the center core are involved in the formation of pseudo-continuous duplex DNA. Four metal-mediated base pairs are observed between the N7 atoms of G and Co II , an interaction that strongly preserves the central junction site. Beyond revealing a new type of ligand-induced, four-way junction, these observations enhance our understanding of the specific supramolecular chemistry of Z1 that is essential for the formation of a noncanonical DNA superstructure. The structural features described here serve as a foundation for the design of new sequence-specific ligands targeting mismatches in the repeat-associated structures.


    Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*(UD)P*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3')A, B, C, D13synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    F1R
    Query on F1R

    Download CCD File 
    A, B, C, D
    N4-[4-[(6-chloranyl-2-methoxy-acridin-9-yl)amino]butyl]-1,3,5-triazine-2,4,6-triamine
    C21 H23 Cl N8 O
    YRQBNFDRSZQBNL-UHFFFAOYSA-N
     Ligand Interaction
    CO
    Query on CO

    Download CCD File 
    A, B
    COBALT (II) ION
    Co
    XLJKHNWPARRRJB-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.55 Å
    • R-Value Free: 0.190 
    • R-Value Work: 0.165 
    • R-Value Observed: 0.168 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 57.204α = 90
    b = 62.631β = 121.29
    c = 29.743γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data scaling
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    SHELXCDphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2020-07-15
      Type: Initial release