DSSR-derived G-quadruplex features in PDB entry 1c38
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>. 3DNA Forum · User Manual · NAR'15 Paper · PyMOL Plugin.
Poster "DSSR-Enabled Automatic Identification and Annotation of G-quadruplexes in the PDB" presented at the RNA2020 online meeting
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
Summary information [schematics · tetrads · helices · stems · costacks · homepage]
- PDB-id
- 1c38
- Class
- DNA
- Method
- NMR
- Summary
- Solution structure of a quadruplex forming DNA and its intermediate
- Reference
- Marathias, V.M., Bolton, P.H.: (2000) "Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA." Nucleic Acids Res., 28, 1969-1977.
- Abstract
- Potassium can stabilize the formation of chair- or edge-type quadruplex DNA structures and appears to be the only naturally occurring cation that can do so. As quadruplex DNAs may be important in the structure of telomere, centromere, triplet repeat and other DNAs, information about the details of the potassium-quadruplex DNA interactions are of interest. The structures of the 1:1 and the fully saturated, 2:1, potassium-DNA complexes of d(GGTTGGTGTGGTTGG) have been determined using the combination of experimental NMR results and restrained molecular dynamics simulations. The refined structures have been used to model the interactions at the potassium binding sites. Comparison of the 1:1 and 2:1 potassium:DNA structures indicates how potassium binding can determine the folding pattern of the DNA. In each binding site potassium interacts with the carbonyl oxygens of both the loop thymine residues and the guanine residues of the adjacent quartet.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(+Ln+Lw+Ln), chair(2+2), UDUD
Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]
List of 2 G-tetrads [summary · schematics · helices · stems · costacks · homepage]
1 glyco-bond=s-s- groove=wnwn planarity=0.557 type=other nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 2 glyco-bond=---s groove=--wn planarity=0.631 type=other nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]
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, 2 G-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5 step#1 mm(<>,outward) area=19.47 rise=3.70 twist=12.7 strand#1 DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2 strand#2 DNA glyco-bond=-- nts=2 GG A.DG15,A.DG14 strand#3 DNA glyco-bond=s- nts=2 GG A.DG10,A.DG11 strand#4 DNA glyco-bond=-s nts=2 GG A.DG6,A.DG5 |
| 1 stacking diagram | |
 |
1 glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 |
List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]
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, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)
 |
1 glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5 step#1 mm(<>,outward) area=19.47 rise=3.70 twist=12.7 strand#1 U DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2 strand#2 D DNA glyco-bond=-- nts=2 GG A.DG15,A.DG14 strand#3 U DNA glyco-bond=s- nts=2 GG A.DG10,A.DG11 strand#4 D DNA glyco-bond=-s nts=2 GG A.DG6,A.DG5 loop#1 type=lateral strands=[#1,#4] nts=2 TT A.DT3,A.DT4 loop#2 type=lateral strands=[#4,#3] nts=3 TGT A.DT7,A.DG8,A.DT9 loop#3 type=lateral strands=[#3,#2] nts=2 TT A.DT12,A.DT13 |