DSSR-enabled G4 identification/annotation: PDB entry 7d5e
Summary information and primary citation
- PDB-id
- 7d5e
- Class
- DNA
- Method
- X-ray (1.296 Å)
- Summary
- Left-handed g-quadruplex containing two bulges
- Reference
- Das P, Ngo KH, Winnerdy FR, Maity A, Bakalar B, Mechulam Y, Schmitt E, Phan AT (2021): "Bulges in left-handed G-quadruplexes." Nucleic Acids Res., 49, 1724-1736. doi: 10.1093/nar/gkaa1259.
- Abstract
- G-quadruplex (G4) DNA structures with a left-handed backbone progression have unique and conserved structural features. Studies on sequence dependency of the structures revealed the prerequisites and some minimal motifs required for left-handed G4 formation. To extend the boundaries, we explore the adaptability of left-handed G4s towards the existence of bulges. Here we present two X-ray crystal structures and an NMR solution structure of left-handed G4s accommodating one, two and three bulges. Bulges in left-handed G4s show distinct characteristics as compared to those in right-handed G4s. The elucidation of intricate structural details will help in understanding the possible roles and limitations of these unique structures.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(+P+P+P), negative twist
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.137 type=planar O+ nts=4 GGGG 1:A.DG1,1:A.DG4,1:A.DG8,1:A.DG12 2 glyco-bond=---- sugar=---- groove=---- planarity=0.027 type=planar O+ nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG10,1:A.DG13 3 glyco-bond=---- sugar=---- groove=---- planarity=0.079 type=planar O+ nts=4 GGGG 1:A.DG15,1:A.DG18,1:A.DG21,1:A.DG24 4 glyco-bond=---- sugar=---- groove=---- planarity=0.197 type=other O+ nts=4 GGGG 1:A.DG17,1:A.DG20,1:A.DG23,1:A.DG26
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, with 1 stem
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG4,1:A.DG8,1:A.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG10,1:A.DG13 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG24,1:A.DG21,1:A.DG18,1:A.DG15 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG23,1:A.DG20,1:A.DG17,1:A.DG26 step#1 mp(<<,backward) area=11.18 rise=3.25 twist=-28.9 step#2 mm(<>,outward) area=29.21 rise=3.30 twist=-10.7 step#3 pm(>>,forward) area=12.14 rise=3.28 twist=-26.0 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG24,1:A.DG23 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG4,1:A.DG6,1:A.DG21,1:A.DG20 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG8,1:A.DG10,1:A.DG18,1:A.DG17 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG12,1:A.DG13,1:A.DG15,1:A.DG26 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG4,1:A.DG8,1:A.DG12 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG10,1:A.DG13 |
|
3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG24,1:A.DG21,1:A.DG18,1: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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, WARNING, 4+0, 2(+P+P+P), WARNING
|
1 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG1,1:A.DG12,1:A.DG8,1:A.DG4 2 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG2,1:A.DG13,1:A.DG10,1:A.DG6 step#1 mp(<<,backward) area=11.18 rise=3.25 twist=-28.9 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG1,1:A.DG2 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG12,1:A.DG13 strand#3* U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG8,1:A.DG10 bulged-nts=1 T 1:A.DT9 strand#4* U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG4,1:A.DG6 bulged-nts=1 T 1:A.DT5 loop#1 type=propeller strands=[#1,#4] nts=1 T 1:A.DT3 loop#2 type=propeller strands=[#4,#3] nts=1 T 1:A.DT7 loop#3 type=propeller strands=[#3,#2] nts=1 T 1:A.DT11 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG 1:A.DG15,1:A.DT16,1:A.DG17,1:A.DG18 2* type=V-shaped helix=#1 nts=4 GGTG 1:A.DG23,1:A.DG24,1:A.DT25,1:A.DG26