DSSR-enabled G4 identification/annotation: PDB entry 9ciy
Summary information and primary citation
- PDB-id
- 9ciy
- Class
- DNA
- Method
- X-ray (2.4 Å)
- Summary
- Right-left hybrid parallel g-quadruplex from nsd1 promoter
- Reference
- Xing ER, Yatsunyk LA: "Structure of a left-right-handed G-quadruplex from the promoter of the NSD1 gene."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.086 type=planar O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 2 glyco-bond=---- sugar=---- groove=---- planarity=0.203 type=other O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 3 glyco-bond=---- sugar=---- groove=---- planarity=0.038 type=planar O+ nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 4 glyco-bond=---- sugar=---. groove=---- planarity=0.132 type=planar O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,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 A.DG3,A.DG6,A.DG9,A.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24 4 glyco-bond=---- sugar=---. groove=---- Major-->WC O+ nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG26 step#1 mp(<<,backward) area=11.03 rise=3.26 twist=-26.5 step#2 mm(<>,outward) area=28.67 rise=3.34 twist=-9.7 step#3 pm(>>,forward) area=9.02 rise=3.24 twist=35.4 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,A.DG21,A.DG22 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG6,A.DG7,A.DG18,A.DG19 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG9,A.DG10,A.DG15,A.DG16 strand#4 DNA glyco-bond=---- sugar=---. nts=4 GGGG A.DG12,A.DG1,A.DG24,A.DG26 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1 |
|
3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24 |
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, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 2 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG26 step#1 pm(>>,forward) area=9.02 rise=3.24 twist=35.4 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG18,A.DG19 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG21,A.DG22 strand#4* U DNA glyco-bond=-- sugar=-. nts=2 GG A.DG24,A.DG26 bulged-nts=1 T A.DT25 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT17 loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT20 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT23 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG A.DG1,A.DT2,A.DG3,A.DG4 2* type=V-shaped helix=#1 nts=4 GGTG A.DG9,A.DG10,A.DT11,A.DG12