DSSR-enabled G4 identification/annotation: PDB entry 2lod
Summary information and primary citation
- PDB-id
- 2lod
- Class
- DNA
- Method
- NMR
- Summary
- Solution-state structure of an intramolecular g-quadruplex with propeller, diagonal and edgewise loops
- Reference
- Marusic M, Sket P, Bauer L, Viglasky V, Plavec J (2012): "Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops." Nucleic Acids Res., 40, 6946-6956. doi: 10.1093/nar/gks329.
- Abstract
- We herein report on the formation and high-resolution NMR solution-state structure determination of a G-quadruplex adopted by d[G(3)ATG(3)ACACAG(4)ACG(3)] comprised of four G-tracts with the third one consisting of four guanines that are intervened with non-G streches of different lengths. A single intramolecular antiparallel (3+1) G-quadruplex exhibits three stacked G-quartets connected with propeller, diagonal and edgewise loops of different lengths. The propeller and edgewise loops are well structured, whereas the longer diagonal loop is more flexible. To the best of our knowledge, this is the first high-resolution G-quadruplex structure where all of the three main loop types are present.
- 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=0.219 type=other N- nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.109 type=planar N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.309 type=bowl N+ nts=4 GGGG A.DG3,A.DG8,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
|
1 glyco-bond=sss- sugar=.--- groove=--wn Major-->WC N- nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14 step#1 mm(<>,outward) area=15.30 rise=3.50 twist=17.7 step#2 pm(>>,forward) area=13.84 rise=3.45 twist=25.1 strand#1 DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 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.DG15,A.DG14 |
| 2 stacking diagrams | |
|
1 glyco-bond=sss- sugar=.--- groove=--wn Major-->WC N- nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16 |
|
2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 |
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.DG1,A.DG6,A.DG20,A.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14 step#1 mm(<>,outward) area=15.30 rise=3.50 twist=17.7 step#2 pm(>>,forward) area=13.84 rise=3.45 twist=25.1 strand#1 U DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG6,A.DG7,A.DG8 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.DG15,A.DG14 loop#1 type=propeller strands=[#1,#2] nts=2 AT A.DA4,A.DT5 loop#2 type=diagonal strands=[#2,#4] nts=5 ACACA A.DA9,A.DC10,A.DA11,A.DC12,A.DA13 loop#3 type=lateral strands=[#4,#3] nts=3 GAC A.DG17,A.DA18,A.DC19 |