Detailed DSSR results for the G-quadruplex: PDB entry 3mij
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
- 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, parallel(4+0), UUUU
Base-block schematics in six views
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-tetrad layers, inter-molecular, with 1 stem
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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 |
| 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 |
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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 |
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=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 |