Summary information and primary citation

PDB-id
3mij
Class
RNA
Method
X-ray (2.6 Å)
Summary
Crystal structure of a telomeric RNA g-quadruplex complexed with an acridine-based ligand.
Reference
Collie GW, Sparapani S, Parkinson GN, Neidle S (2011): "Structural basis of telomeric RNA quadruplex-acridine ligand recognition." J.Am.Chem.Soc., 133, 2721-2728. doi: 10.1021/ja109767y.
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 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.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=3333 groove=---- planarity=0.250 type=other  -- nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.220 type=other  -- nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.225 type=bowl   -- nts=4 GGGG 1:A.G5,1:A.G11,2:A.G5,2:A.G11

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 3 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG 1:A.G5,1:A.G11,2:A.G5,2:A.G11
  step#1  pm(>>,forward)  area=9.09  rise=3.37 twist=32.5
  step#2  pm(>>,forward)  area=15.53 rise=3.61 twist=24.3
  strand#1 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G3,1:A.G4,1:A.G5
  strand#2 RNA glyco-bond=--- sugar=333 nts=3 GGG 1:A.G9,1:A.G10,1:A.G11
  strand#3 RNA glyco-bond=--- sugar=33- nts=3 GGG 2:A.G3,2:A.G4,2:A.G5
  strand#4 RNA glyco-bond=--- sugar=333 nts=3 GGG 2:A.G9,2:A.G10,2:A.G11

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2 stacking diagrams 
 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
  step#1  pm(>>,forward)  area=9.09  rise=3.37 twist=32.5

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 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG 1:A.G5,1:A.G11,2:A.G5,2:A.G11
  step#2  pm(>>,forward)  area=15.53 rise=3.61 twist=24.3

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 3 G-tetrads, 2 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG 1:A.G5,1:A.G11,2:A.G5,2:A.G11
  step#1  pm(>>,forward)  area=9.09  rise=3.37 twist=32.5
  step#2  pm(>>,forward)  area=15.53 rise=3.61 twist=24.3
  strand#1  U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G3,1:A.G4,1:A.G5
  strand#2  U RNA glyco-bond=--- sugar=333 nts=3 GGG 1:A.G9,1:A.G10,1:A.G11
  strand#3  U RNA glyco-bond=--- sugar=33- nts=3 GGG 2:A.G3,2:A.G4,2:A.G5
  strand#4  U RNA glyco-bond=--- sugar=333 nts=3 GGG 2:A.G9,2:A.G10,2:A.G11
  loop#1 type=propeller strands=[#1,#2] nts=3 UUA 1:A.U6,1:A.U7,1:A.A8
  loop#2 type=propeller strands=[#3,#4] nts=3 UUA 2:A.U6,2:A.U7,2:A.A8

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