Summary information [schematics · tetrads · helices · stems · costacks · homepage]

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.
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 · parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=ssss groove=---- planarity=0.163 type=other  nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2
 2 glyco-bond=---- groove=---- planarity=0.255 type=bowl   nts=4 GGGG A.G3,D.G3,B.G3,C.G3
 3 glyco-bond=---- groove=---- planarity=0.268 type=bowl   nts=4 GGGG A.G5,D.G5,B.G5,C.G5
 4 glyco-bond=ssss groove=---- planarity=0.176 type=other  nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2
 5 glyco-bond=---- groove=---- planarity=0.259 type=bowl   nts=4 GGGG E.G3,H.G3,F.G3,G.G3
 6 glyco-bond=---- groove=---- planarity=0.291 type=bowl   nts=4 GGGG E.G5,H.G5,F.G5,G.G5

List of 2 G4-helices [summary · schematics · tetrads · stems · costacks · homepage]

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-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,D.G3,B.G3,C.G3
 3  glyco-bond=---- 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-- nts=3 gGG A.BGM2,A.G3,C.G5
  strand#2 RNA glyco-bond=s-- nts=3 gGG D.BGM2,D.G3,A.G5
  strand#3 RNA glyco-bond=s-- nts=3 gGG B.BGM2,B.G3,D.G5
  strand#4 RNA glyco-bond=s-- nts=3 gGG C.BGM2,C.G3,B.G5

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2 stacking diagrams
 1  glyco-bond=ssss groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2
2 glyco-bond=---- 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

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,D.G3,B.G3,C.G3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.G5,A.G5,D.G5,B.G5
step#2 pm(>>,forward) area=8.23 rise=3.46 twist=-36.7

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Helix#2, 3 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G3,H.G3,F.G3,G.G3
 3  glyco-bond=---- 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-- nts=3 gGG E.BGM2,E.G3,G.G5
  strand#2 RNA glyco-bond=s-- nts=3 gGG H.BGM2,H.G3,E.G5
  strand#3 RNA glyco-bond=s-- nts=3 gGG F.BGM2,F.G3,H.G5
  strand#4 RNA glyco-bond=s-- nts=3 gGG G.BGM2,G.G3,F.G5

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2 stacking diagrams
 1  glyco-bond=ssss groove=---- Major-->WC nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2
2 glyco-bond=---- 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

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G3,H.G3,F.G3,G.G3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG G.G5,E.G5,H.G5,F.G5
step#2 pm(>>,forward) area=7.74 rise=3.49 twist=-37.3

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List of 2 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

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-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,B.BGM2,C.BGM2
 2  glyco-bond=---- 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- nts=2 gG A.BGM2,A.G3
  strand#2  U RNA glyco-bond=s- nts=2 gG D.BGM2,D.G3
  strand#3  U RNA glyco-bond=s- nts=2 gG B.BGM2,B.G3
  strand#4  U RNA glyco-bond=s- nts=2 gG C.BGM2,C.G3

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Stem#2, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 gggg E.BGM2,H.BGM2,F.BGM2,G.BGM2
 2  glyco-bond=---- 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- nts=2 gG E.BGM2,E.G3
  strand#2  U RNA glyco-bond=s- nts=2 gG H.BGM2,H.G3
  strand#3  U RNA glyco-bond=s- nts=2 gG F.BGM2,F.G3
  strand#4  U RNA glyco-bond=s- nts=2 gG G.BGM2,G.G3

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)