DSSR-enabled G4 identification/annotation: PDB entry 7d5d
Summary information and primary citation
- PDB-id
- 7d5d
- Class
- DNA
- Method
- X-ray (1.18 Å)
- Summary
- Left-handed g-quadruplex containing one bulge
- 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=0.144 type=planar O+ nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11 2 glyco-bond=---- sugar=---- groove=---- planarity=0.039 type=planar O+ nts=4 GGGG A.DG2,A.DG6,A.DG9,A.DG12 3 glyco-bond=---- sugar=---- groove=---- planarity=0.084 type=planar O+ nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23 4 glyco-bond=---- sugar=---- groove=---- planarity=0.155 type=planar O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25
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 A.DG1,A.DG4,A.DG8,A.DG11 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG9,A.DG12 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG25 step#1 mp(<<,backward) area=10.83 rise=3.29 twist=-29.3 step#2 mm(<>,outward) area=29.28 rise=3.29 twist=-10.7 step#3 pm(>>,forward) area=12.29 rise=3.33 twist=-25.7 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG23,A.DG22 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG4,A.DG6,A.DG20,A.DG19 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG8,A.DG9,A.DG17,A.DG16 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG11,A.DG12,A.DG14,A.DG25 |
| 3 stacking diagrams | |
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG9,A.DG12 |
|
3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14 |
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 A.DG1,A.DG11,A.DG8,A.DG4 2 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG2,A.DG12,A.DG9,A.DG6 step#1 mp(<<,backward) area=10.83 rise=3.29 twist=-29.3 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG1,A.DG2 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG11,A.DG12 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9 strand#4* U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG4,A.DG6 bulged-nts=1 T A.DT5 loop#1 type=propeller strands=[#1,#4] nts=1 T A.DT3 loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT7 loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT10 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG A.DG14,A.DT15,A.DG16,A.DG17 2* type=V-shaped helix=#1 nts=4 GGTG A.DG22,A.DG23,A.DT24,A.DG25