Detailed DSSR results for the G-quadruplex: PDB entry 2grb
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
- 2grb
- Class
- RNA
- Method
- X-ray (1.4 Å)
- Summary
- Crystal structure of an RNA quadruplex containing inosine-tetrad
- Reference
- Pan B, Shi K, Sundaralingam M (2006): "Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads." J.Mol.Biol., 363, 451-459. doi: 10.1016/j.jmb.2006.08.022.
- Abstract
- Polyinosinic acid has been known to adopt the four-stranded helical structure but its basic unit, inosine tetrad (I tetrad), has not been determined at the atomic level. Here we report the crystal structure of an RNA quadruplex containing an I tetrad at 1.4 A resolution. The I tetrad has one cyclic hydrogen bond N1...O6 with the bond length of 2.7 A. A water bridge is observed in the minor groove side of the base tetrad. Even though it is sandwiched by guanine tetrads (G tetrads), the I tetrad is buckled towards the 3' side of the tetrad plane, which results from the different interaction strength with K ions on two sides of the tetrad plane. Comparison with both G tetrad and adenine tetrad indicates that lack of NH2 in the C2 position makes the I tetrad prone to buckle for interactions with ligands. Two U*(G-G-G-G) base pentads are observed at the junction of the 5' termini of two quadruplexes. The uridine residue in the base pentad is engaged in two hydrogen bonding interactions (N2(G)-H...O2(U) and O2'(G)-H...O4(U)) and a water-mediated interaction (N3(G) and N3(U)) with the G tetrad. We also discuss the roles of amino group in purine tetrads and the inter-quadruplex interactions in RNA molecules. These quadruplexes may interact with each other by stacking, groove binding and intercalation.
- G4 notes
- 8 G-tetrads, 2 G4 helices, 2 G4 stems, parallel(4+0), UUUU
Base-block schematics in six views
List of 8 G-tetrads
1 glyco-bond=---- sugar=3333 groove=---- planarity=0.322 type=other nts=4 GGGG A.G2,D.G2,B.G2,C.G2 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.327 type=other nts=4 gggg A.I3,D.I3,B.I3,C.I3 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.175 type=other nts=4 GGGG A.G4,D.G4,B.G4,C.G4 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.189 type=other nts=4 GGGG A.G5,D.G5,B.G5,C.G5 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.262 type=other nts=4 GGGG E.G2,H.G2,F.G2,G.G2 6 glyco-bond=---- sugar=3333 groove=---- planarity=0.279 type=other nts=4 gggg E.I3,H.I3,F.I3,G.I3 7 glyco-bond=---- sugar=3333 groove=---- planarity=0.140 type=planar nts=4 GGGG E.G4,H.G4,F.G4,G.G4 8 glyco-bond=---- sugar=3333 groove=---- planarity=0.255 type=bowl nts=4 GGGG E.G5,H.G5,F.G5,G.G5
List of 2 G4-helices
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, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,D.G2,B.G2,C.G2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.I3,D.I3,B.I3,C.I3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,D.G4,B.G4,C.G4 4 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G5,D.G5,B.G5,C.G5 step#1 pm(>>,forward) area=12.12 rise=3.27 twist=32.1 step#2 pm(>>,forward) area=6.59 rise=3.48 twist=29.1 step#3 pm(>>,forward) area=14.38 rise=3.66 twist=23.6 strand#1 RNA glyco-bond=---- sugar=3333 nts=4 GgGG A.G2,A.I3,A.G4,A.G5 strand#2 RNA glyco-bond=---- sugar=3333 nts=4 GgGG D.G2,D.I3,D.G4,D.G5 strand#3 RNA glyco-bond=---- sugar=3333 nts=4 GgGG B.G2,B.I3,B.G4,B.G5 strand#4 RNA glyco-bond=---- sugar=3333 nts=4 GgGG C.G2,C.I3,C.G4,C.G5 |
| 3 stacking diagrams | |
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,D.G2,B.G2,C.G2 |
 |
2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.I3,D.I3,B.I3,C.I3 |
 |
3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,D.G4,B.G4,C.G4 |
Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G2,H.G2,F.G2,G.G2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.I3,H.I3,F.I3,G.I3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G4,H.G4,F.G4,G.G4 4 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G5,H.G5,F.G5,G.G5 step#1 pm(>>,forward) area=11.61 rise=3.28 twist=32.0 step#2 pm(>>,forward) area=6.20 rise=3.50 twist=29.3 step#3 pm(>>,forward) area=14.30 rise=3.72 twist=23.3 strand#1 RNA glyco-bond=---- sugar=3333 nts=4 GgGG E.G2,E.I3,E.G4,E.G5 strand#2 RNA glyco-bond=---- sugar=3333 nts=4 GgGG H.G2,H.I3,H.G4,H.G5 strand#3 RNA glyco-bond=---- sugar=3333 nts=4 GgGG F.G2,F.I3,F.G4,F.G5 strand#4 RNA glyco-bond=---- sugar=3333 nts=4 GgGG G.G2,G.I3,G.G4,G.G5 |
| 3 stacking diagrams | |
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G2,H.G2,F.G2,G.G2 |
 |
2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.I3,H.I3,F.I3,G.I3 |
 |
3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G4,H.G4,F.G4,G.G4 |
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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,D.G2,B.G2,C.G2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.I3,D.I3,B.I3,C.I3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,D.G4,B.G4,C.G4 4 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G5,D.G5,B.G5,C.G5 step#1 pm(>>,forward) area=12.12 rise=3.27 twist=32.1 step#2 pm(>>,forward) area=6.59 rise=3.48 twist=29.1 step#3 pm(>>,forward) area=14.38 rise=3.66 twist=23.6 strand#1 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG A.G2,A.I3,A.G4,A.G5 strand#2 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG D.G2,D.I3,D.G4,D.G5 strand#3 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG B.G2,B.I3,B.G4,B.G5 strand#4 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG C.G2,C.I3,C.G4,C.G5 |
Stem#2, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G2,H.G2,F.G2,G.G2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.I3,H.I3,F.I3,G.I3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G4,H.G4,F.G4,G.G4 4 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G5,H.G5,F.G5,G.G5 step#1 pm(>>,forward) area=11.61 rise=3.28 twist=32.0 step#2 pm(>>,forward) area=6.20 rise=3.50 twist=29.3 step#3 pm(>>,forward) area=14.30 rise=3.72 twist=23.3 strand#1 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG E.G2,E.I3,E.G4,E.G5 strand#2 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG H.G2,H.I3,H.G4,H.G5 strand#3 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG F.G2,F.I3,F.G4,F.G5 strand#4 U RNA glyco-bond=---- sugar=3333 nts=4 GgGG G.G2,G.I3,G.G4,G.G5 |