DSSR-derived G-quadruplex features in PDB entry 1n7a
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
- 1n7a
- Class
- DNA, RNA
- Method
- X-ray (1.2 Å)
- Summary
- Rip-radiation-damage induced phasing
- Reference
- Ravelli, R.B.G., Leiros, H.-K.S., Pan, B., Caffrey, M., McSweeney, S.: (2003) "Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures." Structure, 11, 217-224.
- Abstract
- The use of third generation synchrotron sources has led to renewed concern about the effect of ionizing radiation on crystalline biological samples. In general, the problem is seen as one to be avoided. However, in this paper, it is shown that, far from being a hindrance to successful structure determination, radiation damage provides an opportunity for phasing macromolecular structures. This is successfully demonstrated for both a protein and an oligonucleotide, by way of which complete models were built automatically. The possibility that, through the exploitation of radiation damage, the phase problem could become less of a barrier to macromolecular crystal structure determination is discussed.
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 5'/5'-SEPARATED
Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]
List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]
1 glyco-bond=---- groove=---- planarity=0.101 type=planar nts=4 gggg A.BGM2,C.BGM2,H.BGM2,D.BGM2 2 glyco-bond=---- groove=---- planarity=0.154 type=planar nts=4 GGGG A.G4,C.G4,H.G4,D.G4 3 glyco-bond=---- groove=---- planarity=0.277 type=bowl nts=4 GGGG A.G5,C.G5,H.G5,D.G5 4 glyco-bond=---- groove=---- planarity=0.088 type=planar nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2 5 glyco-bond=---- groove=---- planarity=0.153 type=planar nts=4 GGGG B.G4,E.G4,F.G4,G.G4 6 glyco-bond=---- groove=---- planarity=0.261 type=bowl nts=4 GGGG B.G5,E.G5,F.G5,G.G5
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, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5 2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4 3 glyco-bond=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2 4 glyco-bond=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2 5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4 6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G5,G.G5,F.G5,E.G5 step#1 mp(<<,backward) area=14.29 rise=3.66 twist=21.8 step#2 mp(<<,backward) area=0.00 rise=6.65 twist=149.4 step#3 mm(<>,outward) area=31.88 rise=3.38 twist=-15.6 step#4 pm(>>,forward) area=0.00 rise=6.64 twist=-31.0 step#5 pm(>>,forward) area=13.57 rise=3.62 twist=22.5 strand#1 RNA glyco-bond=------ nts=6 GGggGG A.G5,A.G4,A.BGM2,B.BGM2,B.G4,B.G5 strand#2 RNA glyco-bond=------ nts=6 GGggGG C.G5,C.G4,D.BGM2,E.BGM2,G.G4,G.G5 strand#3 RNA glyco-bond=------ nts=6 GGggGG H.G5,H.G4,H.BGM2,F.BGM2,F.G4,F.G5 strand#4 RNA glyco-bond=------ nts=6 GGggGG D.G5,D.G4,C.BGM2,G.BGM2,E.G4,E.G5 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5 |
 |
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4 |
 |
3 glyco-bond=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2 |
 |
4 glyco-bond=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2 |
 |
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4 |
List of 2 G4-stems [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, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4 2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5 step#1 pm(>>,forward) area=14.29 rise=3.66 twist=21.8 strand#1 U RNA glyco-bond=-- nts=2 GG A.G4,A.G5 strand#2 U RNA glyco-bond=-- nts=2 GG C.G4,C.G5 strand#3 U RNA glyco-bond=-- nts=2 GG H.G4,H.G5 strand#4 U RNA glyco-bond=-- nts=2 GG D.G4,D.G5 |
Stem#2, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G4,E.G4,F.G4,G.G4 2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G5,E.G5,F.G5,G.G5 step#1 pm(>>,forward) area=13.57 rise=3.62 twist=22.5 strand#1 U RNA glyco-bond=-- nts=2 GG B.G4,B.G5 strand#2 U RNA glyco-bond=-- nts=2 GG E.G4,E.G5 strand#3 U RNA glyco-bond=-- nts=2 GG F.G4,F.G5 strand#4 U RNA glyco-bond=-- nts=2 GG G.G4,G.G5 |
List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5'-SEPARATED]