Detailed DSSR results for the G-quadruplex: PDB entry 2kbp
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
- 2kbp
- Class
- RNA
- Method
- NMR
- Summary
- Solution structure of a g-quadruplex of human telomeric RNA
- Reference
- Martadinata H, Phan AT (2009): "Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution." J.Am.Chem.Soc., 131, 2570-2578. doi: 10.1021/ja806592z.
- Abstract
- Very recent studies showed that mammalian telomeres were transcribed into telomeric-repeat-containing RNAs and suggested that these RNA molecules were biologically important. Here we report on a structural study of RNA G-quadruplexes formed by human telomeric RNA sequences in K(+) solution. Our data indicated that these sequences formed propeller-type parallel-stranded RNA G-quadruplexes. We have determined the NMR-based solution structure of a dimeric propeller-type RNA G-quadruplex formed by the 12-nt human telomeric RNA sequence r(UAGGGUUAGGGU). We also observed the stacking of two such propeller-type G-quadruplex blocks for the 10-nt human telomeric RNA sequence r(GGGUUAGGGU) and a higher-order G-quadruplex structure for the 9-nt human telomeric RNA sequence r(GGGUUAGGG). Based on these findings we proposed how higher-order structures might be formed by long telomeric RNA.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.234 type=other nts=4 GGGG A.G3,A.G9,B.G15,B.G21 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.169 type=other nts=4 GGGG A.G4,A.G10,B.G16,B.G22 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.246 type=other nts=4 GGGG A.G5,A.G11,B.G17,B.G23
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, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G15,B.G21 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,A.G10,B.G16,B.G22 3 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G5,A.G11,B.G17,B.G23 step#1 pm(>>,forward) area=8.17 rise=3.71 twist=33.8 step#2 pm(>>,forward) area=14.42 rise=4.29 twist=26.5 strand#1 RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G3,A.G4,A.G5 strand#2 RNA glyco-bond=--- sugar=-33 nts=3 GGG A.G9,A.G10,A.G11 strand#3 RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G15,B.G16,B.G17 strand#4 RNA glyco-bond=--- sugar=-33 nts=3 GGG B.G21,B.G22,B.G23 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G15,B.G21 |
 |
2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,A.G10,B.G16,B.G22 |
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, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G15,B.G21 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,A.G10,B.G16,B.G22 3 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G5,A.G11,B.G17,B.G23 step#1 pm(>>,forward) area=8.17 rise=3.71 twist=33.8 step#2 pm(>>,forward) area=14.42 rise=4.29 twist=26.5 strand#1 U RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G3,A.G4,A.G5 strand#2 U RNA glyco-bond=--- sugar=-33 nts=3 GGG A.G9,A.G10,A.G11 strand#3 U RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G15,B.G16,B.G17 strand#4 U RNA glyco-bond=--- sugar=-33 nts=3 GGG B.G21,B.G22,B.G23 loop#1 type=propeller strands=[#1,#2] nts=3 UUA A.U6,A.U7,A.A8 loop#2 type=propeller strands=[#3,#4] nts=3 UUA B.U18,B.U19,B.A20 |