Detailed DSSR results for the G-quadruplex: PDB entry 7x7g
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
- 7x7g
- Class
- DNA
- Method
- X-ray (2.19 Å)
- Summary
- Crystal structure of a dimeric interlocked parallel g-quadruplex
- Reference
- Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT (2022): "Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A.G.G.G.G pentad in an interlocked G-quadruplex." Biochem.Biophys.Res.Commun., 613, 153-158. doi: 10.1016/j.bbrc.2022.04.020.
- Abstract
- 93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K+ solution. Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. While confirming the overall dimeric interlocked G-quadruplex folding topology previously determined by NMR, our results reveal important detailed structural information, particularly the formation of a water-mediated A•G•G•G•G pentad. These insights allow us to better understand the formation of various structural elements in G-quadruplexes and should be useful for designing and manipulating G-quadruplex scaffolds with desired properties.
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'-SEPARATED
Base-block schematics in six views
List of 6 G-tetrads
1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.099 type=planar nts=4 GGGG A.DG1,B.DG6,B.DG2,B.DG13 2 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.097 type=planar nts=4 GGGG A.DG2,A.DG6,B.DG1,A.DG13 3 glyco-bond=---- sugar=--.- groove=---- planarity=0.143 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14 4 glyco-bond=---- sugar=---- groove=---- planarity=0.298 type=other nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15 5 glyco-bond=---- sugar=--.- groove=---- planarity=0.142 type=planar nts=4 GGGG B.DG3,B.DG7,B.DG10,B.DG14 6 glyco-bond=---- sugar=---. groove=---- planarity=0.312 type=bowl nts=4 GGGG B.DG4,B.DG8,B.DG11,B.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, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15 2 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14 3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG1,A.DG13 4 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG6,B.DG2,B.DG13 5 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG7,B.DG3,B.DG14 6 glyco-bond=---- sugar=---. groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,B.DG4,B.DG15 step#1 mp(<<,backward) area=11.81 rise=3.34 twist=29.1 step#2 mp(<<,backward) area=7.42 rise=3.33 twist=33.1 step#3 mm(<>,outward) area=12.07 rise=3.58 twist=20.1 step#4 pm(>>,forward) area=7.83 rise=3.31 twist=32.5 step#5 pm(>>,forward) area=10.30 rise=3.37 twist=29.9 strand#1 DNA glyco-bond=---s-- sugar=----.- nts=6 GGGGGG A.DG4,A.DG3,A.DG2,A.DG1,B.DG10,B.DG11 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG8,A.DG7,A.DG6,B.DG6,B.DG7,B.DG8 strand#3 DNA glyco-bond=--s--- sugar=-.---- nts=6 GGGGGG A.DG11,A.DG10,B.DG1,B.DG2,B.DG3,B.DG4 strand#4 DNA glyco-bond=------ sugar=-----. nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG13,B.DG14,B.DG15 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15 |
 |
2 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG10,A.DG14 |
 |
3 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG1,A.DG13 |
 |
4 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG6,B.DG2,B.DG13 |
 |
5 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG B.DG10,B.DG7,B.DG3,B.DG14 |
List of 2 G4-stems
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.DG3,A.DG7,A.DG10,A.DG14 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG15 step#1 pm(>>,forward) area=11.81 rise=3.34 twist=29.1 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.DG10,A.DG11 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG14,A.DG15 loop#1 type=propeller strands=[#1,#2] nts=2 TG A.DT5,A.DG6 loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA9 loop#3 type=propeller strands=[#3,#4] nts=2 TG A.DT12,A.DG13 |
Stem#2, 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 B.DG3,B.DG7,B.DG10,B.DG14 2 glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG11,B.DG15 step#1 pm(>>,forward) area=10.30 rise=3.37 twist=29.9 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG3,B.DG4 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG7,B.DG8 strand#3 U DNA glyco-bond=-- sugar=.- nts=2 GG B.DG10,B.DG11 strand#4 U DNA glyco-bond=-- sugar=-. nts=2 GG B.DG14,B.DG15 loop#1 type=propeller strands=[#1,#2] nts=2 TG B.DT5,B.DG6 loop#2 type=propeller strands=[#2,#3] nts=1 A B.DA9 loop#3 type=propeller strands=[#3,#4] nts=2 TG B.DT12,B.DG13 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5'-SEPARATED]