Detailed DSSR results for the G-quadruplex: PDB entry 2ld8
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
- 2ld8
- Class
- DNA
- Method
- NMR
- Summary
- Structure of human telomeric DNA in crowded solution
- Reference
- Heddi B, Phan AT (2011): "Structure of Human Telomeric DNA in Crowded Solution." J.Am.Chem.Soc. doi: 10.1021/ja200786q.
- Abstract
- G-quadruplex structures formed by DNA at the human telomeres are attractive anticancer targets. Human telomeric sequences can adopt a diverse range of intramolecular G-quadruplex conformations: a parallel-stranded conformation was observed in the crystalline state, while at least four other forms were seen in K(+) solution, raising the question of which conformation is favored in crowded cellular environment. Here, we report the first NMR structure of a human telomeric G-quadruplex in crowded solution. We show that four different G-quadruplex conformations are converted to a propeller-type parallel-stranded G-quadruplex in K(+)-containing crowded solution due to water depletion. This study also reveals the formation of a new higher-order G-quadruplex structure under molecular crowding conditions. Our molecular dynamics simulations of solvent distribution provide insights at molecular level on the formation of parallel-stranded G-quadruplex in environment depleted of water. These results regarding human telomeric DNA can be extended to oncogenic promoters and other genomic G-rich sequences.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=.--- groove=---- planarity=0.331 type=other nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 2 glyco-bond=---- sugar=...- groove=---- planarity=0.442 type=bowl-2 nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=---- sugar=---- groove=---- planarity=0.458 type=bowl nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
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, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 2 glyco-bond=---- sugar=...- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 step#1 pm(>>,forward) area=13.97 rise=3.33 twist=23.1 step#2 pm(>>,forward) area=11.58 rise=3.28 twist=30.7 strand#1 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG15,A.DG16,A.DG17 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG21,A.DG22,A.DG23 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 |
 |
2 glyco-bond=---- sugar=...- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 |
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, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 2 glyco-bond=---- sugar=...- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 step#1 pm(>>,forward) area=13.97 rise=3.33 twist=23.1 step#2 pm(>>,forward) area=11.58 rise=3.28 twist=30.7 strand#1 U DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG15,A.DG16,A.DG17 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG21,A.DG22,A.DG23 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=propeller strands=[#2,#3] nts=3 TTA A.DT12,A.DT13,A.DA14 loop#3 type=propeller strands=[#3,#4] nts=3 TTA A.DT18,A.DT19,A.DA20 |