Detailed DSSR results for the G-quadruplex: PDB entry 2lby
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
- 2lby
- Class
- DNA
- Method
- NMR
- Summary
- G-quadruplex structure formed at the 5'-end of nheiii_1 element in human c-myc promoter
- Reference
- Mathad RI, Hatzakis E, Dai J, Yang D (2011): "c-MYC promoter G-quadruplex formed at the 5'-end of NHE III1 element: insights into biological relevance and parallel-stranded G-quadruplex stability." Nucleic Acids Res., 39, 9023-9033. doi: 10.1093/nar/gkr612.
- Abstract
- We studied the structures and stabilities of G-quadruplexes formed in Myc1234, the region containing the four consecutive 5' runs of guanines of c-MYC promoter NHE III(1,) which have recently been shown to form in a supercoiled plasmid system in aqueous solution. We determined the NMR solution structure of the 1:2:1 parallel-stranded loop isomer, one of the two major loop isomers formed in Myc1234 in K(+) solution. This major loop isomer, although sharing the same folding structure, appears to be markedly less stable than the major loop isomer formed in the single-stranded c-MYC NHE III(1) oligonucleotide, the Myc2345 G-quadruplex. Our NMR structures indicated that the different thermostabilities of the two 1:2:1 parallel c-MYC G-quadruplexes are likely caused by the different base conformations of the single nucleotide loops. The observation of the formation of the Myc1234 G-quadruplex in the supercoiled plasmid thus points to the potential role of supercoiling in the G-quadruplex formation in promoter sequences. We also performed a systematic thermodynamic analysis of modified c-MYC NHE III(1) sequences, which provided quantitative measure of the contributions of various loop sequences to the thermostabilities of parallel-stranded G-quadruplexes. This information is important for understanding the equilibrium of promoter G-quadruplex loop isomers and for their drug targeting.
- 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=0.071 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16 2 glyco-bond=---- sugar=.... groove=---- planarity=0.120 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 3 glyco-bond=---- sugar=..-. groove=---- planarity=0.152 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
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.DG7,A.DG12,A.DG16 2 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 3 glyco-bond=---- sugar=..-. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 step#1 pm(>>,forward) area=12.55 rise=3.84 twist=29.3 step#2 pm(>>,forward) area=17.18 rise=3.97 twist=26.8 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.DG7,A.DG8,A.DG9 strand#3 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG12,A.DG13,A.DG14 strand#4 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG16,A.DG17,A.DG18 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16 |
 |
2 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 |
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.DG7,A.DG12,A.DG16 2 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 3 glyco-bond=---- sugar=..-. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 step#1 pm(>>,forward) area=12.55 rise=3.84 twist=29.3 step#2 pm(>>,forward) area=17.18 rise=3.97 twist=26.8 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.DG7,A.DG8,A.DG9 strand#3 U DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG12,A.DG13,A.DG14 strand#4 U DNA glyco-bond=--- sugar=... nts=3 GGG A.DG16,A.DG17,A.DG18 loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA6 loop#2 type=propeller strands=[#2,#3] nts=2 TA A.DT10,A.DA11 loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA15 |