DSSR-enabled G4 identification/annotation: PDB entry 4u5m
Summary information and primary citation
- PDB-id
- 4u5m
- Class
- DNA
- Method
- X-ray (1.5 Å)
- Summary
- Structure of a left-handed DNA g-quadruplex
- Reference
- Chung WJ, Heddi B, Schmitt E, Lim KW, Mechulam Y, Phan AT (2015): "Structure of a left-handed DNA G-quadruplex." Proc.Natl.Acad.Sci.USA, 112, 2729-2733. doi: 10.1073/pnas.1418718112.
- Abstract
- Aside from the well-known double helix, DNA can also adopt an alternative four-stranded structure known as G-quadruplex. Implications of such a structure in cellular processes, as well as its therapeutic and diagnostic applications, have been reported. The G-quadruplex structure is highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of a left-handed DNA G-quadruplex. The structure displays unprecedented features that can be exploited as unique recognition elements.
- 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=s--- sugar=---- groove=w--n planarity=0.219 type=other O+ nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5 2 glyco-bond=---- sugar=---- groove=---- planarity=0.079 type=planar O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 3 glyco-bond=---- sugar=---- groove=---- planarity=0.088 type=planar O+ nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 4 glyco-bond=---- sugar=---- groove=---- planarity=0.193 type=other O+ nts=4 GGGG A.DG17,A.DG20,A.DG23,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=s--- sugar=---- groove=w--n Major-->WC O+ nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5 2 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG24,A.DG15,A.DG18,A.DG21 4 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG23,A.DG26,A.DG17,A.DG20 step#1 mp(<<,backward) area=10.88 rise=3.29 twist=-28.1 step#2 mm(<>,outward) area=29.32 rise=3.30 twist=-10.9 step#3 pm(>>,forward) area=12.02 rise=3.29 twist=-25.8 strand#1 DNA glyco-bond=s--- sugar=---- nts=4 GGGG A.DG2,A.DG3,A.DG24,A.DG23 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG11,A.DG12,A.DG15,A.DG26 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG8,A.DG9,A.DG18,A.DG17 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG5,A.DG6,A.DG21,A.DG20 |
| 3 stacking diagrams | |
|
1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC O+ nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5 |
|
2 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG24,A.DG15,A.DG18,A.DG21 |
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=s--- sugar=---- groove=w--n Major-->WC O+ nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5 2 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6 step#1 mp(<<,backward) area=10.88 rise=3.29 twist=-28.1 strand#1 U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG2,A.DG3 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.DG5,A.DG6 loop#1 type=propeller strands=[#1,#4] nts=1 T A.DT4 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.DG15,A.DT16,A.DG17,A.DG18 2* type=V-shaped helix=#1 nts=4 GGTG A.DG23,A.DG24,A.DT25,A.DG26