Summary information [schematics · tetrads · helices · stems · costacks · homepage]

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, G.W., Sparapani, S., Parkinson, G.N., Neidle, S.: (2011) "Structural basis of telomeric RNA quadruplex-acridine ligand recognition." J.Am.Chem.Soc., 133, 2721-2728.
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 · parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.250 type=other  nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 2 glyco-bond=---- groove=---- planarity=0.220 type=other  nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 3 glyco-bond=---- 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 [summary · schematics · tetrads · stems · costacks · homepage]

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-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 3  glyco-bond=---- 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=--- nts=3 GGG 1:A.G3,1:A.G4,1:A.G5
  strand#2 RNA glyco-bond=--- nts=3 GGG 1:A.G9,1:A.G10,1:A.G11
  strand#3 RNA glyco-bond=--- nts=3 GGG 2:A.G3,2:A.G4,2:A.G5
  strand#4 RNA glyco-bond=--- nts=3 GGG 2:A.G9,2:A.G10,2:A.G11

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
2 glyco-bond=---- 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=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
3 glyco-bond=---- 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 [summary · schematics · tetrads · helices · costacks · homepage]

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-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 3  glyco-bond=---- 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=--- nts=3 GGG 1:A.G3,1:A.G4,1:A.G5
  strand#2  U RNA glyco-bond=--- nts=3 GGG 1:A.G9,1:A.G10,1:A.G11
  strand#3  U RNA glyco-bond=--- nts=3 GGG 2:A.G3,2:A.G4,2:A.G5
  strand#4  U RNA glyco-bond=--- 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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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)