Detailed DSSR results for the G-quadruplex: PDB entry 1kf1
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
- 1kf1
- Class
- DNA
- Method
- X-ray (2.1 Å)
- Summary
- Structure and packing of human telomeric DNA
- Reference
- Parkinson GN, Lee MP, Neidle S (2002): "Crystal structure of parallel quadruplexes from human telomeric DNA." Nature, 417, 876-880. doi: 10.1038/nature755.
- Abstract
- Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, are fundamental in protecting the cell from recombination and degradation. Disruption of telomere maintenance leads to eventual cell death, which can be exploited for therapeutic intervention in cancer. Telomeric DNA sequences can form four-stranded (quadruplex) structures, which may be involved in the structure of telomere ends. Here we describe the crystal structure of a quadruplex formed from four consecutive human telomeric DNA repeats and grown at a K(+) concentration that approximates its intracellular concentration. K(+) ions are observed in the structure. The folding and appearance of the DNA in this intramolecular quadruplex is fundamentally different from the published Na(+)-containing quadruplex structures. All four DNA strands are parallel, with the three linking trinucleotide loops positioned on the exterior of the quadruplex core, in a propeller-like arrangement. The adenine in each TTA linking trinucleotide loop is swung back so that it intercalates between the two thymines. This DNA structure suggests a straightforward path for telomere folding and unfolding, as well as ways in which it can recognize telomere-associated proteins.
- 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=0.074 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 2 glyco-bond=---- sugar=---- groove=---- planarity=0.187 type=other nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 3 glyco-bond=---- sugar=---- groove=---- planarity=0.309 type=bowl nts=4 GGGG A.DG4,A.DG10,A.DG16,A.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, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 step#1 pm(>>,forward) area=11.44 rise=3.44 twist=28.3 step#2 pm(>>,forward) area=9.82 rise=3.48 twist=28.9 strand#1 DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.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, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 step#1 pm(>>,forward) area=11.44 rise=3.44 twist=28.3 step#2 pm(>>,forward) area=9.82 rise=3.48 twist=28.9 strand#1 U DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT5,A.DT6,A.DA7 loop#2 type=propeller strands=[#2,#3] nts=3 TTA A.DT11,A.DT12,A.DA13 loop#3 type=propeller strands=[#3,#4] nts=3 TTA A.DT17,A.DT18,A.DA19 |