Detailed DSSR results for the G-quadruplex: PDB entry 2n21
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
- 2n21
- Class
- hydrolase-DNA
- Method
- NMR
- Summary
- Solution structure of complex between DNA g-quadruplex and g-quadruplex recognition domain of rhau
- Reference
- Heddi B, Cheong VV, Martadinata H, Phan AT (2015): "Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex." Proc.Natl.Acad.Sci.USA, 112, 9608-9613. doi: 10.1073/pnas.1422605112.
- Abstract
- Four-stranded nucleic acid structures called G-quadruplexes have been associated with important cellular processes, which should require G-quadruplex-protein interaction. However, the structural basis for specific G-quadruplex recognition by proteins has not been understood. The DEAH (Asp-Glu-Ala-His) box RNA helicase associated with AU-rich element (RHAU) (also named DHX36 or G4R1) specifically binds to and resolves parallel-stranded G-quadruplexes. Here we identified an 18-amino acid G-quadruplex-binding domain of RHAU and determined the structure of this peptide bound to a parallel DNA G-quadruplex. Our structure explains how RHAU specifically recognizes parallel G-quadruplexes. The peptide covers a terminal guanine base tetrad (G-tetrad), and clamps the G-quadruplex using three-anchor-point electrostatic interactions between three positively charged amino acids and negatively charged phosphate groups. This binding mode is strikingly similar to that of most ligands selected for specific G-quadruplex targeting. Binding to an exposed G-tetrad represents a simple and efficient way to specifically target G-quadruplex structures.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.225 type=other nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15 2 glyco-bond=---- sugar=---- groove=---- planarity=0.150 type=planar nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16 3 glyco-bond=---- sugar=---- groove=---- planarity=0.194 type=other nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
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 B.DG3,B.DG7,B.DG11,B.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17 step#1 pm(>>,forward) area=9.62 rise=3.35 twist=33.8 step#2 pm(>>,forward) area=14.15 rise=3.35 twist=31.4 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG3,B.DG4,B.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16 |
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, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17 step#1 pm(>>,forward) area=9.62 rise=3.35 twist=33.8 step#2 pm(>>,forward) area=14.15 rise=3.35 twist=31.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG3,B.DG4,B.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT6 loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT10 loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT14 |