DSSR-derived G-quadruplex features in PDB entry 6gzn
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
- 6gzn
- Class
- DNA
- Method
- NMR
- Summary
- Adenine-driven structural switch from two- to three-quartet DNA G-quadruplex
- Reference
- Lenarcic Zivkovic, M., Rozman, J., Plavec, J.: (2018) "Adenine-Driven Structural Switch from a Two- to Three-Quartet DNA G-Quadruplex." Angew. Chem. Int. Ed. Engl., 57, 15395-15399.
- Abstract
- A G-rich sequence found in the regulatory region of the RANKL gene, which is associated with homeostasis of bone metabolism, folds into a two-quartet basket-type G-quadruplex stabilized by A⋅G⋅A and G⋅G⋅G base-triads. Perusal of local structural features together with G/A-to-T modifications uncovered the critical role of A5 for the formation of a distinct antiparallel two-quartet topology and not the three-quartet topology that would be expected based on the sequence with four GGG-tracts alone. The structural changes induced by the A5-to-T5 modification include a switch in orientation and relative positions of G-strands that together with anti to syn reorientation of G12 provide insights into the complexity of the interactions that influence the folding of G-rich DNA. Understanding the impact of loop residues on the stability and formation of G-quadruplexes advances our knowledge and ability to predict structures adopted by G-rich sequences, which are involved in regulatory mechanisms in the cell, and may also facilitate drug design.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-LwD+Ln), basket(2+2), UDDU
Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]
List of 2 G-tetrads [summary · schematics · helices · stems · costacks · homepage]
1 glyco-bond=s--s groove=w-n- planarity=0.086 type=planar nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13 2 glyco-bond=-ss- groove=w-n- planarity=0.129 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG18,A.DG14
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, 2 G-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13 2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG18,A.DG14 step#1 mm(<>,outward) area=16.89 rise=3.44 twist=16.6 strand#1 DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2 strand#2 DNA glyco-bond=-s nts=2 GG A.DG7,A.DG6 strand#3 DNA glyco-bond=-s nts=2 GG A.DG19,A.DG18 strand#4 DNA glyco-bond=s- nts=2 GG A.DG13,A.DG14 |
| 1 stacking diagram | |
 |
1 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13 |
List of 1 G4-stem [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, 3 loops, INTRA-molecular, UDDU, anti-parallel, 2(-LwD+Ln), basket(2+2)
 |
1 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG19,A.DG13 2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG18,A.DG14 step#1 mm(<>,outward) area=16.89 rise=3.44 twist=16.6 strand#1 U DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2 strand#2 D DNA glyco-bond=-s nts=2 GG A.DG7,A.DG6 strand#3 D DNA glyco-bond=-s nts=2 GG A.DG19,A.DG18 strand#4 U DNA glyco-bond=s- nts=2 GG A.DG13,A.DG14 loop#1 type=lateral strands=[#1,#2] nts=3 GTA A.DG3,A.DT4,A.DA5 loop#2 type=diagonal strands=[#2,#4] nts=5 GAGCG A.DG8,A.DA9,A.DG10,A.DC11,A.DG12 loop#3 type=lateral strands=[#4,#3] nts=3 AGA A.DA15,A.DG16,A.DA17 |