Detailed DSSR results for the G-quadruplex: PDB entry 3qcr
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- 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, parallel(4+0), UUUU
Base-block schematics in six views
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-tetrad layers, inter-molecular, with 1 stem
 |
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-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, 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 |