3QCR

Incomplete structural model of a human telomeric DNA quadruplex-acridine complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.378 
  • R-Value Work: 0.344 
  • R-Value Observed: 0.346 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of telomeric RNA quadruplex-acridine ligand recognition.

Collie, G.W.Sparapani, S.Parkinson, G.N.Neidle, S.

(2011) J Am Chem Soc 133: 2721-2728

  • DOI: 10.1021/ja109767y
  • Primary Citation of Related Structures:  
    3QCR, 3MIJ

  • PubMed Abstract: 
  • Human telomeric DNA is now known to be transcribed into noncoding RNA sequences, termed TERRA. These sequences, which are believed to play roles in the regulation of telomere function, can form higher-order quadruplex structures and may themselves be ...

    Human telomeric DNA is now known to be transcribed into noncoding RNA sequences, termed TERRA. These sequences, which are believed to play roles in the regulation of telomere function, can form higher-order quadruplex structures and may themselves be the target of therapeutic intervention. The crystal structure of a TERRA quadruplex-acridine small-molecule complex at a resolution of 2.60 Å, is reported here and contrasts remarkably with the structure of the analogous DNA quadruplex complex. The bimolecular RNA complex has a parallel-stranded topology with propeller-like UUA loops. These loops are held in particular conformations by multiple hydrogen bonds involving the O2' hydroxyl groups of the ribonucleotide sugars and play an active role in binding the acridine molecules to the RNA quadruplex. By contrast, the analogous DNA quadruplex complex has simpler 1:1 acridine binding, with no loop involvement. There are significant loop conformational changes in the RNA quadruplex compared to the native TERRA quadruplex (Collie, G. W.; Haider, S. M.; Neidle, S.; Parkinson, G. N. Nucleic Acids Res. 2010, 38, 5569 - 5580), which have implications for the future design of small molecules targeting TERRA quadruplexes, and RNA quadruplexes more generally.


    Organizational Affiliation

    CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, United Kingdom.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    Human telomeric repeat deoxyribonucleic acidA12Homo sapiens
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    R14
    Query on R14

    Download CCD File 
    A
    N,N'-[acridine-3,6-diylbis(1H-1,2,3-triazole-1,4-diylbenzene-3,1-diyl)]bis[3-(diethylamino)propanamide]
    C43 H47 N11 O2
    HZKPUBMHIBOFRM-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download CCD File 
    A
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.378 
    • R-Value Work: 0.344 
    • R-Value Observed: 0.346 
    • Space Group: P 62 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 71.674α = 90
    b = 71.674β = 90
    c = 29.37γ = 120
    Software Package:
    Software NamePurpose
    DNAdata collection
    PHASERphasing
    REFMACrefinement
    XDSdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2011-02-16
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance