Detailed DSSR results for the G-quadruplex: PDB entry 2o3m
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
- 2o3m
- Class
- DNA
- Method
- NMR
- Summary
- Monomeric g-DNA tetraplex from human c-kit promoter
- Reference
- Phan AT, Kuryavyi VV, Burge S, Neidle S, Patel DJ (2007): "Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter." J.Am.Chem.Soc., 129, 4386-4392. doi: 10.1021/ja068739h.
- Abstract
- The c-kit oncogene is an important target in the treatment of gastrointestinal tumors. A potential approach to inhibition of the expression of this gene involves selective stabilization of G-quadruplex structures that may be induced to form in the c-kit promoter region. Here we report on the structure of an unprecedented intramolecular G-quadruplex formed by a G-rich sequence in the c-kit promoter in K+ solution. The structure represents a new folding topology with several unique features. Most strikingly, an isolated guanine is involved in G-tetrad core formation, despite the presence of four three-guanine tracts. There are four loops: two single-residue double-chain-reversal loops, a two-residue loop, and a five-residue stem-loop, which contain base-pairing alignments. This unique structural scaffold provides a highly specific platform for the future design of ligands specifically targeted to the promoter DNA of c-kit.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-PX+P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13 2 glyco-bond=---- sugar=---- groove=---- planarity=0.112 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 3 glyco-bond=---- sugar=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
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.DG6,A.DG10,A.DG13 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15 step#1 pm(>>,forward) area=13.74 rise=3.14 twist=27.9 step#2 pm(>>,forward) area=10.77 rise=3.19 twist=32.0 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.DG6,A.DG7,A.DG8 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG10,A.DG21,A.DG22 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 |
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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-PX+P), parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15 step#1 pm(>>,forward) area=10.77 rise=3.19 twist=32.0 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG3,A.DG4 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG21,A.DG22 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG14,A.DG15 loop#1 type=propeller strands=[#1,#2] nts=2 AG A.DA5,A.DG6 loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG A.DC9,A.DG10,A.DC11,A.DT12,A.DG13 loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG A.DA16,A.DG17,A.DG18,A.DA19,A.DG20 |
List of 2 non-stem G4-loops (including the two closing Gs)
1* type=V-shaped helix=#1 nts=5 GGGCG A.DG6,A.DG7,A.DG8,A.DC9,A.DG10 2 type=lateral helix=#1 nts=4 GCTG A.DG10,A.DC11,A.DT12,A.DG13