DSSR-enabled G4 identification/annotation: PDB entry 6kvb
Summary information and primary citation
- PDB-id
- 6kvb
- Class
- DNA
- Method
- NMR
- Summary
- Structure of an intra-locked g-quadruplex
- Reference
- Maity A, Winnerdy FR, Chang WD, Chen G, Phan AT (2020): "Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs." Nucleic Acids Res., 48, 3315-3327. doi: 10.1093/nar/gkaa008.
- Abstract
- G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.
- G4 notes
- 4 G-tetrads, 1 G4 helix
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=s--- sugar=3--- groove=w--n planarity=0.044 type=planar O+ nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6 2 glyco-bond=---- sugar=---- groove=---- planarity=0.094 type=planar O+ nts=4 GGGG A.DG3,A.DG17,A.DG20,A.DG23 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.075 type=planar O+ nts=4 GGGG A.DG5,A.DG8,A.DG11,A.DG15 4 glyco-bond=---s sugar=---3 groove=--wn planarity=0.023 type=planar O+ nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27
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, 4 G-tetrads, INTRA-molecular
|
1 glyco-bond=s--- sugar=3--- groove=w--n Major-->WC O+ nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6 2 glyco-bond=s--- sugar=---- groove=w--n Major-->WC O+ nts=4 GGGG A.DG15,A.DG11,A.DG8,A.DG5 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG3 4 glyco-bond=---s sugar=---3 groove=--wn WC-->Major O+ nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27 step#1 mp(<<,backward) area=8.89 rise=3.40 twist=32.9 step#2 mm(<>,outward) area=10.15 rise=3.92 twist=23.1 step#3 pm(>>,forward) area=8.09 rise=3.21 twist=32.2 strand#1 DNA glyco-bond=ss-- sugar=3--- nts=4 GGGG A.DG2,A.DG15,A.DG17,A.DG18 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG20,A.DG21 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG9,A.DG8,A.DG23,A.DG24 strand#4 DNA glyco-bond=---s sugar=---3 nts=4 GGGG A.DG6,A.DG5,A.DG3,A.DG27 |
| 3 stacking diagrams | |
|
1 glyco-bond=s--- sugar=3--- groove=w--n Major-->WC O+ nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6 |
|
2 glyco-bond=s--- sugar=---- groove=w--n Major-->WC O+ nts=4 GGGG A.DG15,A.DG11,A.DG8,A.DG5 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG3 |
List of 3 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=5 GGTGG A.DG2,A.DG3,A.DT4,A.DG5,A.DG6 2* type=V-shaped helix=#1 nts=5 GGTTG A.DG11,A.DG12,A.DT13,A.DT14,A.DG15 3 type=lateral helix=#1 nts=4 GTTG A.DG24,A.DT25,A.DT26,A.DG27