DSSR-enabled G4 identification/annotation: PDB entry 3qcr
Summary information and primary citation
- PDB-id
- 3qcr
- Class
- DNA
- Method
- X-ray (3.2 Å)
- Summary
- Incomplete structural model of a human telomeric DNA quadruplex-acridine complex.
- 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)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.143 type=planar -- nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 2 glyco-bond=---- sugar=---- groove=---- planarity=0.223 type=other -- nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 3 glyco-bond=---- sugar=.-.- groove=---- planarity=0.306 type=bowl -- nts=4 GGGG 1:A.DG5,1:A.DG11,2:A.DG5,2:A.DG11
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
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:A.DG11,2:A.DG5,2:A.DG11 step#1 pm(>>,forward) area=11.74 rise=3.41 twist=28.7 step#2 pm(>>,forward) area=8.76 rise=3.22 twist=28.2 strand#1 DNA glyco-bond=--- sugar=--. nts=3 GGG 1:A.DG3,1:A.DG4,1:A.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11 strand#3 DNA glyco-bond=--- sugar=--. nts=3 GGG 2:A.DG3,2:A.DG4,2:A.DG5 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 |
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=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:A.DG11,2:A.DG5,2:A.DG11 step#1 pm(>>,forward) area=11.74 rise=3.41 twist=28.7 step#2 pm(>>,forward) area=8.76 rise=3.22 twist=28.2 strand#1 U DNA glyco-bond=--- sugar=--. nts=3 GGG 1:A.DG3,1:A.DG4,1:A.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11 strand#3 U DNA glyco-bond=--- sugar=--. nts=3 GGG 2:A.DG3,2:A.DG4,2:A.DG5 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11 loop#1 type=propeller strands=[#1,#2] nts=3 TTA 1:A.DT6,1:A.DT7,1:A.DA8 loop#2 type=propeller strands=[#3,#4] nts=3 TTA 2:A.DT6,2:A.DT7,2:A.DA8 |