DSSR-enabled G4 identification/annotation: PDB entry 8pse
Summary information and primary citation
- PDB-id
- 8pse
- Class
- DNA
- Method
- NMR
- Summary
- (3+1) hybrid g-quadruplex from a g-rich sequence with five g-runs
- Reference
- Vianney YM, Schroder N, Jana J, Chojetzki G, Weisz K (2023): "Showcasing Different G-Quadruplex Folds of a G-Rich Sequence: Between Rule-Based Prediction and Butterfly Effect." J.Am.Chem.Soc., 145, 22194-22205. doi: 10.1021/jacs.3c08336.
- Abstract
- In better understanding the interactions of G-quadruplexes in a cellular or noncellular environment, a reliable sequence-based prediction of their three-dimensional fold would be extremely useful, yet is often limited by their remarkable structural diversity. A G-rich sequence related to a promoter sequence of the PDGFR-β nuclease hypersensitivity element (NHE) comprises a G<sub>3</sub>-G<sub>3</sub>-G<sub>2</sub>-G<sub>4</sub>-G<sub>3</sub> pattern of five G-runs with two to four G residues. Although the predominant formation of three-layered canonical G-quadruplexes with uninterrupted G-columns can be expected, minimal base substitutions in a non-G-tract domain were shown to guide folding into either a basket-type antiparallel quadruplex, a parallel-stranded quadruplex with an interrupted G-column, a quadruplex with a V-shaped loop, or a (3+1) hybrid quadruplex. A 3D NMR structure for each of the different folds was determined. Supported by thermodynamic profiling on additional sequence variants, formed topologies were rationalized by the identification and assessment of specific critical interactions of loop and overhang residues, giving valuable insights into their contribution to favor a particular conformer. The variability of such tertiary interactions, together with only small differences in quadruplex free energies, emphasizes current limits for a reliable sequence-dependent prediction of favored topologies from sequences with multiple irregularly positioned G-tracts.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 3(-PD+Lw)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=sss- sugar=.--- groove=--wn planarity=0.307 type=saddle N- nts=4 GGGG A.DG2,A.DG7,A.DG20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.337 type=other N+ nts=4 GGGg A.DG3,A.DG8,A.DG21,A.BGM15 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.303 type=other N+ nts=4 GGGG A.DG4,A.DG9,A.DG22,A.DG14
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-tetrads, INTRA-molecular, with 1 stem
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1 glyco-bond=sss- sugar=.--- groove=--wn Major-->WC N- nts=4 GGGG A.DG2,A.DG7,A.DG20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGg A.DG3,A.DG8,A.DG21,A.BGM15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG9,A.DG22,A.DG14 step#1 mm(<>,outward) area=15.56 rise=3.50 twist=19.0 step#2 pm(>>,forward) area=11.86 rise=3.42 twist=27.2 strand#1 DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GgG A.DG16,A.BGM15,A.DG14 |
| 2 stacking diagrams | |
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1 glyco-bond=sss- sugar=.--- groove=--wn Major-->WC N- nts=4 GGGG A.DG2,A.DG7,A.DG20,A.DG16 |
|
2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGg A.DG3,A.DG8,A.DG21,A.BGM15 |
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-tetrads, 3 loops, INTRA-molecular, UUUD, hybrid2, 3+1, 3(-PD+Lw)
|
1 glyco-bond=sss- sugar=.--- groove=--wn Major-->WC N- nts=4 GGGG A.DG2,A.DG7,A.DG20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGg A.DG3,A.DG8,A.DG21,A.BGM15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG9,A.DG22,A.DG14 step#1 mm(<>,outward) area=15.56 rise=3.50 twist=19.0 step#2 pm(>>,forward) area=11.86 rise=3.42 twist=27.2 strand#1 U DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 strand#4 D DNA glyco-bond=-ss sugar=--- nts=3 GgG A.DG16,A.BGM15,A.DG14 loop#1 type=propeller strands=[#1,#2] nts=2 TA A.DT5,A.DA6 loop#2 type=diagonal strands=[#2,#4] nts=4 CGGC A.DC10,A.DG11,A.DG12,A.DC13 loop#3 type=lateral strands=[#4,#3] nts=3 TAC A.DT17,A.DA18,A.DC19 |