3MIJ

Crystal structure of a telomeric RNA G-quadruplex complexed with an acridine-based ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.235 

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:  

  • 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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')A12Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
R14
Query on R14

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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]
triazole-acridine conjugate
C43 H47 N11 O2
HZKPUBMHIBOFRM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.235 
  • Space Group: P 2 3
Unit Cell:
Length (Å)Angle (°)
a = 56.606α = 90.00
b = 56.606β = 90.00
c = 56.606γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
CrystalCleardata scaling
CrystalCleardata reduction
DNAdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

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