Detailed DSSR results for the G-quadruplex: PDB entry 1oz8
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
- 1oz8
- Class
- DNA
- Method
- NMR
- Summary
- Intramolecular higher-order packing of parallel quadruplexes comprising a g:g:g:g tetrad and a g(:a):g(:a):g(:a):g heptad of gga triplet repeat DNA
- Reference
- Matsugami A, Okuizumi T, Uesugi S, Katahira M (2003): "Intramolecular Higher Order Packing of Parallel Quadruplexes Comprising a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad of GGA Triplet Repeat DNA." J.BIOL.CHEM., 278, 28147-28153. doi: 10.1074/jbc.M303694200.
- Abstract
- GGA triplet repeats are widely dispersed throughout eukaryotic genomes and are frequently located within biologically important regions such as gene regulatory regions and recombination hot spot sites. We determined the structure of d(GGA)4 (12-mer) under physiological conditions and founded the formation of an intramolecular parallel quadruplex for the first time. Later, a similar architecture to that of the intramolecular parallel quadruplex was found for a telomere DNA in the crystalline state. Here, we have determined the structure of d(GGA)8 (24-mer) under physiological conditions. Two intramolecular parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad are formed in d(GGA)8. These quadruplexes are packed in a tail-to-tail manner. This is the first demonstration of the intramolecular higher order packing of quadruplexes at atomic resolution. K+ ions, but not Na+ ones, are critically required for the formation of this unique structure. The elucidated structure suggests the mechanisms underlying the biological events related to the GGA triplet repeat. Furthermore, in the light of the structure, the mode of the higher order packing of the telomere DNA is discussed.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=-... groove=---- planarity=0.322 type=other nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 2 glyco-bond=---- sugar=.... groove=---- planarity=0.381 type=other nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22 3 glyco-bond=---- sugar=---. groove=---- planarity=0.522 type=bowl nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23
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.DG1,A.DG4,A.DG7,A.DG10 2 glyco-bond=---- sugar=.... groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG13 3 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14 step#1 mm(<>,outward) area=26.12 rise=3.52 twist=-1.3 step#2 pm(>>,forward) area=9.52 rise=3.27 twist=30.8 strand#1 DNA glyco-bond=--- sugar=-.. nts=3 GGG A.DG1,A.DG22,A.DG23 strand#2 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG4,A.DG19,A.DG20 strand#3 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG7,A.DG16,A.DG17 strand#4 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG10,A.DG13,A.DG14 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=-... groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 |
 |
2 glyco-bond=---- sugar=.... groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG13 |
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(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22 2 glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23 step#1 pm(>>,forward) area=9.52 rise=3.27 twist=30.8 strand#1 U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG13,A.DG14 strand#2 U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG16,A.DG17 strand#3 U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG19,A.DG20 strand#4 U DNA glyco-bond=-- sugar=.. nts=2 GG A.DG22,A.DG23 loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA15 loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA18 loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA21 |
List of 3 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=4 GGAG A.DG1,A.DG2,A.DA3,A.DG4 2 type=lateral helix=#1 nts=4 GGAG A.DG4,A.DG5,A.DA6,A.DG7 3 type=lateral helix=#1 nts=4 GGAG A.DG7,A.DG8,A.DA9,A.DG10