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

PDB-id
1rau
Class
RNA
Method
NMR
Summary
Solution structure of an unusually stable RNA tetraplex containing g-and u-quartet structures
Reference
Cheong, C., Moore, P.B.: (1992) "Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures." Biochemistry, 31, 8406-8414.
Abstract
A model for the solution structure of an RNA tetraplex, (rUGGGGU)4, has been obtained by two-dimensional NMR spectroscopy and molecular dynamics. The molecule is parallel stranded and Hoogsteen base-paired in 50 mM KCl, and it is so stable that three of its six imino protons have exchange half-lives measured in days at 40 degrees C. The tetraplex is stabilized by base stacking and by the hydrogen bonds in four G quartets and at least one U quartet. This is the first indication of the existence of U-quartet structures of which we are aware.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · 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 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.105 type=planar nts=4 GGGG A.G2,B.G2,C.G2,D.G2
 2 glyco-bond=---- groove=---- planarity=0.056 type=planar nts=4 GGGG A.G3,B.G3,C.G3,D.G3
 3 glyco-bond=---- groove=---- planarity=0.063 type=planar nts=4 GGGG A.G4,B.G4,C.G4,D.G4
 4 glyco-bond=---- groove=---- planarity=0.078 type=planar nts=4 GGGG A.G5,B.G5,C.G5,D.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, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,B.G2,C.G2,D.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,B.G3,C.G3,D.G3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,B.G4,C.G4,D.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,B.G5,C.G5,D.G5
  step#1  pm(>>,forward)  area=13.89 rise=3.12 twist=26.9
  step#2  pm(>>,forward)  area=9.79  rise=4.30 twist=35.4
  step#3  pm(>>,forward)  area=18.71 rise=4.23 twist=24.8
  strand#1 RNA glyco-bond=---- nts=4 GGGG A.G2,A.G3,A.G4,A.G5
  strand#2 RNA glyco-bond=---- nts=4 GGGG B.G2,B.G3,B.G4,B.G5
  strand#3 RNA glyco-bond=---- nts=4 GGGG C.G2,C.G3,C.G4,C.G5
  strand#4 RNA glyco-bond=---- nts=4 GGGG D.G2,D.G3,D.G4,D.G5

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,B.G2,C.G2,D.G2
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,B.G3,C.G3,D.G3
step#1 pm(>>,forward) area=13.89 rise=3.12 twist=26.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,B.G3,C.G3,D.G3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,B.G4,C.G4,D.G4
step#2 pm(>>,forward) area=9.79 rise=4.30 twist=35.4

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,B.G4,C.G4,D.G4
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,B.G5,C.G5,D.G5
step#3 pm(>>,forward) area=18.71 rise=4.23 twist=24.8

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,B.G2,C.G2,D.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,B.G3,C.G3,D.G3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,B.G4,C.G4,D.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,B.G5,C.G5,D.G5
  step#1  pm(>>,forward)  area=13.89 rise=3.12 twist=26.9
  step#2  pm(>>,forward)  area=9.79  rise=4.30 twist=35.4
  step#3  pm(>>,forward)  area=18.71 rise=4.23 twist=24.8
  strand#1  U RNA glyco-bond=---- nts=4 GGGG A.G2,A.G3,A.G4,A.G5
  strand#2  U RNA glyco-bond=---- nts=4 GGGG B.G2,B.G3,B.G4,B.G5
  strand#3  U RNA glyco-bond=---- nts=4 GGGG C.G2,C.G3,C.G4,C.G5
  strand#4  U RNA glyco-bond=---- nts=4 GGGG D.G2,D.G3,D.G4,D.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)