DSSR-enabled G4 identification/annotation: PDB entry 2awe
Summary information and primary citation
- PDB-id
- 2awe
- Class
- RNA
- Method
- X-ray (2.1 Å)
- Summary
- Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of i-motif RNA octaplex
- Reference
- Pan B, Shi K, Sundaralingam M (2006): "Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex." Proc.Natl.Acad.Sci.Usa, 103, 3130-3134. doi: 10.1073/pnas.0507730103.
- Abstract
- Nucleic acids adopt different multistranded helical architectures to perform various biological functions. Here, we report a crystal structure of an RNA quadruplex containing "base-tetrad swapping" and bulged nucleotide at 2.1-Angstroms resolution. The base-tetrad swapping results in a dimer of quadruplexes with an intercalated octaplex fragment at the 5' end junction. The intercalated base tetrads provide the basic repeat unit for constructing a model of intercalated RNA octaplex. The model we obtained shows fundamentally different characteristics from duplex, triplex, and quadruplex. We also observed two different orientations of bulged uridine residues that are related to the interaction with surroundings. This structural evidence reflects the conformational flexibility of bulged nucleotides in RNA quadruplexes and implies the potential roles of bulged nucleotides as recognition and interaction sites in RNA-protein and RNA-RNA interactions.
- G4 notes
- 6 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
List of 6 G-tetrads
1 glyco-bond=ssss sugar=---- groove=---- planarity=0.163 type=other -- nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2 2 glyco-bond=---- sugar=---- groove=---- planarity=0.255 type=bowl -- nts=4 GGGG A.G3,D.G3,B.G3,C.G3 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.268 type=bowl -- nts=4 GGGG A.G5,D.G5,B.G5,C.G5 4 glyco-bond=ssss sugar=---- groove=---- planarity=0.176 type=other -- nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2 5 glyco-bond=---- sugar=---- groove=---- planarity=0.259 type=bowl -- nts=4 GGGG E.G3,H.G3,F.G3,G.G3 6 glyco-bond=---- sugar=3333 groove=---- planarity=0.291 type=bowl -- nts=4 GGGG E.G5,H.G5,F.G5,G.G5
List of 2 G4-helices
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, inter-molecular, with 1 stem
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G3,D.G3,B.G3,C.G3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG C.G5,A.G5,D.G5,B.G5 step#1 mm(<>,outward) area=21.61 rise=3.62 twist=15.2 step#2 pm(>>,forward) area=8.23 rise=3.46 twist=-36.7 strand#1 RNA glyco-bond=s-- sugar=--3 nts=3 gGG A.BGM2,A.G3,C.G5 strand#2 RNA glyco-bond=s-- sugar=--3 nts=3 gGG D.BGM2,D.G3,A.G5 strand#3 RNA glyco-bond=s-- sugar=--3 nts=3 gGG B.BGM2,B.G3,D.G5 strand#4 RNA glyco-bond=s-- sugar=--3 nts=3 gGG C.BGM2,C.G3,B.G5 |
| 2 stacking diagrams | |
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G3,D.G3,B.G3,C.G3 |
Helix#2, 3 G-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG E.G3,H.G3,F.G3,G.G3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG G.G5,E.G5,H.G5,F.G5 step#1 mm(<>,outward) area=21.14 rise=3.62 twist=15.9 step#2 pm(>>,forward) area=7.74 rise=3.49 twist=-37.3 strand#1 RNA glyco-bond=s-- sugar=--3 nts=3 gGG E.BGM2,E.G3,G.G5 strand#2 RNA glyco-bond=s-- sugar=--3 nts=3 gGG H.BGM2,H.G3,E.G5 strand#3 RNA glyco-bond=s-- sugar=--3 nts=3 gGG F.BGM2,F.G3,H.G5 strand#4 RNA glyco-bond=s-- sugar=--3 nts=3 gGG G.BGM2,G.G3,F.G5 |
| 2 stacking diagrams | |
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG E.G3,H.G3,F.G3,G.G3 |
List of 2 G4-stems
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, 0 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G3,D.G3,B.G3,C.G3 step#1 mm(<>,outward) area=21.61 rise=3.62 twist=15.2 strand#1 U RNA glyco-bond=s- sugar=-- nts=2 gG A.BGM2,A.G3 strand#2 U RNA glyco-bond=s- sugar=-- nts=2 gG D.BGM2,D.G3 strand#3 U RNA glyco-bond=s- sugar=-- nts=2 gG B.BGM2,B.G3 strand#4 U RNA glyco-bond=s- sugar=-- nts=2 gG C.BGM2,C.G3 |
Stem#2, 2 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG E.G3,H.G3,F.G3,G.G3 step#1 mm(<>,outward) area=21.14 rise=3.62 twist=15.9 strand#1 U RNA glyco-bond=s- sugar=-- nts=2 gG E.BGM2,E.G3 strand#2 U RNA glyco-bond=s- sugar=-- nts=2 gG H.BGM2,H.G3 strand#3 U RNA glyco-bond=s- sugar=-- nts=2 gG F.BGM2,F.G3 strand#4 U RNA glyco-bond=s- sugar=-- nts=2 gG G.BGM2,G.G3 |