Detailed DSSR results for the G-quadruplex: PDB entry 6zrm
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
- 6zrm
- Class
- DNA
- Method
- NMR
- Summary
- G-quadruplex with a g-a bulge
- Reference
- Lenarcic Zivkovic M, Rozman J, Plavec J (2020): "Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming a Pseudo-loop ." Molecules, 25. doi: 10.3390/molecules25204867.
- Abstract
- Bone remodeling is a fine-tuned process principally regulated by a cascade triggered by interaction of receptor activator of NF-κB (RANK) and RANK ligand (RANKL). Excessive activity of the RANKL gene leads to increased bone resorption and can influence the incidence of osteoporosis. Although much has been learned about the intracellular signals activated by RANKL/RANK complex, significantly less is known about the molecular mechanisms of regulation of RANKL expression. Here, we report on the structure of an unprecedented DNA G-quadruplex, well-known secondary structure-mediated gene expression regulator, formed by a G-rich sequence found in the regulatory region of a RANKL gene. Solution-state NMR structural study reveals the formation of a three-layered parallel-type G-quadruplex characterized by an unique features, including a G-A bulge. Although a guanine within a G-tract occupies syn glycosidic conformation, bulge-forming residues arrange in a pseudo-loop conformation to facilitate partial 5/6-ring stacking, typical of G-quadruplex structures with parallel G-tracts orientation. Such distinctive structural features protruding from the core of the structure can represent a novel platform for design of highly specific ligands with anti-osteoporotic function. Additionally, our study suggests that the expression of RANKL gene may be regulated by putative folding of its G-rich region into non-B-DNA structure(s).
- 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=0.262 type=other nts=4 GGGG A.DG2,A.DG6,A.DG12,A.DG18 2 glyco-bond=---- sugar=---- groove=---- planarity=0.185 type=other nts=4 GGGG A.DG3,A.DG7,A.DG13,A.DG19 3 glyco-bond=--s- sugar=--.- groove=-wn- planarity=0.138 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20
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 A.DG2,A.DG6,A.DG12,A.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG13,A.DG19 3 glyco-bond=--s- sugar=--.- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20 step#1 pm(>>,forward) area=14.82 rise=3.47 twist=23.0 step#2 pm(>>,forward) area=9.11 rise=3.39 twist=29.9 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#3 DNA glyco-bond=--s sugar=--. nts=3 GGG A.DG12,A.DG13,A.DG16 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG12,A.DG18 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG13,A.DG19 |
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 A.DG2,A.DG6,A.DG12,A.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG13,A.DG19 3 glyco-bond=--s- sugar=--.- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20 step#1 pm(>>,forward) area=14.82 rise=3.47 twist=23.0 step#2 pm(>>,forward) area=9.11 rise=3.39 twist=29.9 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#3* U DNA glyco-bond=--s sugar=--. nts=3 GGG A.DG12,A.DG13,A.DG16 bulged-nts=2 GA A.DG14,A.DA15 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20 loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA5 loop#2 type=propeller strands=[#2,#3] nts=3 AGC A.DA9,A.DG10,A.DC11 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT17 |