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

PDB-id
1j6s*
Class
RNA
Method
X-ray (1.4 Å)
Summary
Crystal structure of an RNA tetraplex (ugaggu)4 with a-tetrads, G-tetrads, u-tetrads and g-u octads
Reference
Pan, B., Xiong, Y., Shi, K., Deng, J., Sundaralingam, M.: (2003) "Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes." Structure, 11, 815-823.
Abstract
Purine-rich regions in DNA and RNA may contain both guanines and adenines, which have various biological functions. Here we report the crystal structure of an RNA purine-rich fragment containing both guanine and adenine at 1.4 A resolution. Adenines form an adenine tetrad in the N6-H em leader N7 conformation. Substitution of an adenine tetrad in the guanine tetraplex does not change the global conformation but introduces irregularity in both the hydrogen bonding interaction pattern in the groove and the metal ion binding pattern in the central cavity of the tetraplex. The irregularity in groove binding may be critical for specific binding in tetraplexes. The formation of G-U octads provides a mechanism for interaction in the groove. Ba(2+) ions prefer to bind guanine tetrads, and adenine tetrads can only be bound by Na(+) ions, illustrating the binding selectivity of metal ions for the tetraplex.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU

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

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List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.101 type=planar nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
 2 glyco-bond=---- groove=---- planarity=0.067 type=planar nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 3 glyco-bond=---- groove=---- planarity=0.285 type=bowl   nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5

List of 1 G4-helix [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=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
  step#1  pm(>>,forward)  area=0.00  rise=6.71 twist=63.9
  step#2  pm(>>,forward)  area=13.73 rise=3.54 twist=24.9
  strand#1 RNA glyco-bond=--- nts=3 GGG 1:A.G2,1:A.G4,1:A.G5
  strand#2 RNA glyco-bond=--- nts=3 GGG 4:A.G2,4:A.G4,4:A.G5
  strand#3 RNA glyco-bond=--- nts=3 GGG 2:A.G2,2:A.G4,2:A.G5
  strand#4 RNA glyco-bond=--- nts=3 GGG 3:A.G2,3:A.G4,3:A.G5

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
step#1 pm(>>,forward) area=0.00 rise=6.71 twist=63.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
step#2 pm(>>,forward) area=13.73 rise=3.54 twist=24.9

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List of 1 G4-stem [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=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
  step#1  pm(>>,forward)  area=13.73 rise=3.54 twist=24.9
  strand#1  U RNA glyco-bond=-- nts=2 GG 1:A.G4,1:A.G5
  strand#2  U RNA glyco-bond=-- nts=2 GG 4:A.G4,4:A.G5
  strand#3  U RNA glyco-bond=-- nts=2 GG 2:A.G4,2:A.G5
  strand#4  U RNA glyco-bond=-- nts=2 GG 3:A.G4,3:A.G5

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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)