Detailed DSSR results for the G-quadruplex: PDB entry 2hri
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
- 2hri
- Class
- DNA
- Method
- X-ray (2.09 Å)
- Summary
- A parallel stranded human telomeric quadruplex in complex with the porphyrin tmpyp4
- Reference
- Parkinson GN, Ghosh R, Neidle S (2007): "Structural basis for binding of porphyrin to human telomeres." Biochemistry, 46, 2390-2397. doi: 10.1021/bi062244n.
- Abstract
- Maintenance of telomere integrity is a hallmark of human cancer, and the single-stranded 3' ends of telomeric DNA are targets for small-molecule anticancer therapies. We report here the crystal structure of a bimolecular human telomeric quadruplex, of the sequence d(TAGGGTTAGGG), in a complex with the quadruplex-binding ligand 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) to a resolution of 2.09 A. The DNA quadruplex topology is parallel-stranded with external double-chain-reversal propeller loops, consistent with previous structural determinations. The porphyrin molecules bind by stacking onto the TTA nucleotides, either as part of the external loop structure or at the 5' region of the stacked quadruplex. This involves stacked on hydrogen-bonded base pairs, formed from those nucleotides not involved in the formation of G-tetrads, and there are thus no direct ligand interactions with G-tetrads. This is in accord with the relative nonselectivity by TMPyP4 for quadruplex DNAs compared to duplex DNA. Porphyrin binding is achieved by remodeling of loops compared to the ligand-free structures. Implications for the design of quadruplex-binding ligands are discussed, together with a model for the formation of anaphase bridges, which are observed following cellular treatment with TMPyP4.
- 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=0.153 type=planar nts=4 GGGG A.DG3,A.DG9,B.DG14,B.DG20 2 glyco-bond=---- sugar=-.-- groove=---- planarity=0.092 type=planar nts=4 GGGG A.DG4,A.DG10,B.DG15,B.DG21 3 glyco-bond=---- sugar=-.-- groove=---- planarity=0.065 type=planar nts=4 GGGG A.DG5,A.DG11,B.DG16,B.DG22
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 A.DG3,A.DG9,B.DG14,B.DG20 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG15,B.DG21 3 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG16,B.DG22 step#1 pm(>>,forward) area=15.09 rise=3.32 twist=25.2 step#2 pm(>>,forward) area=12.36 rise=3.31 twist=29.3 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 B.DG14,B.DG15,B.DG16 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG20,B.DG21,B.DG22 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG14,B.DG20 |
 |
2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG15,B.DG21 |
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 A.DG3,A.DG9,B.DG14,B.DG20 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG15,B.DG21 3 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG16,B.DG22 step#1 pm(>>,forward) area=15.09 rise=3.32 twist=25.2 step#2 pm(>>,forward) area=12.36 rise=3.31 twist=29.3 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 B.DG14,B.DG15,B.DG16 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG20,B.DG21,B.DG22 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=propeller strands=[#3,#4] nts=3 TTA B.DT17,B.DT18,B.DA19 |