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PDB-id
1j8g*
Class
RNA
Method
X-ray (0.61 Å)
Summary
X-ray analysis of a RNA tetraplex r(uggggu)4 at ultra-high resolution
Reference
Deng, J., Xiong, Y., Sundaralingam, M.: (2001) "X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A)." Proc.Natl.Acad.Sci.USA, 98, 13665-13670.
Abstract
Four-stranded guanine tetraplexes in RNA have been identified to be involved in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)(4) at ultra-high resolution (0.61 A). The space group is P42(1)2, and cell constants are a = b = 36.16 A and c = 74.09 A. The structure was solved by the multiple-wavelength anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative (br)UGGGGU and refined to 0.61-A resolution. Each of the four strands in the asymmetric unit forms a parallel tetraplex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudocontinuous column. All of the 5'-end uridines rotate around the backbone of G2, swing out, and form unique octaplexes with the neighboring G tetraplexes, whereas the 3'-end uridines are stacked-in and form uridine tetrads. All of the bases are anti, and the riboses are in the mixed C2'- and C3'-puckering mode. Strontium ions are observed in every other guanine tetrad plane, sitting on the fourfold axis and associated to the eight O6 atoms of neighboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens are clearly observed in the structure.
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]

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List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.238 type=other  nts=4 GGGG 1:A.G2,3:A.G2,2:A.G2,4:A.G2
 2 glyco-bond=---- groove=---- planarity=0.246 type=bowl   nts=4 GGGG 1:A.G3,3:A.G3,2:A.G3,4:A.G3
 3 glyco-bond=---- groove=---- planarity=0.123 type=planar nts=4 GGGG 1:A.G4,3:A.G4,2:A.G4,4:A.G4
 4 glyco-bond=---- groove=---- planarity=0.295 type=bowl   nts=4 GGGG 1:A.G5,3:A.G5,2:A.G5,4: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, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,3:A.G2,2:A.G2,4:A.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,3:A.G3,2:A.G3,4:A.G3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,3:A.G4,2:A.G4,4:A.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,3:A.G5,2:A.G5,4:A.G5
  step#1  pm(>>,forward)  area=11.74 rise=3.47 twist=27.5
  step#2  pm(>>,forward)  area=8.71  rise=3.15 twist=35.4
  step#3  pm(>>,forward)  area=12.54 rise=3.52 twist=25.2
  strand#1 RNA glyco-bond=---- nts=4 GGGG 1:A.G2,1:A.G3,1:A.G4,1:A.G5
  strand#2 RNA glyco-bond=---- nts=4 GGGG 3:A.G2,3:A.G3,3:A.G4,3:A.G5
  strand#3 RNA glyco-bond=---- nts=4 GGGG 2:A.G2,2:A.G3,2:A.G4,2:A.G5
  strand#4 RNA glyco-bond=---- nts=4 GGGG 4:A.G2,4:A.G3,4:A.G4,4:A.G5

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,3:A.G2,2:A.G2,4:A.G2
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,3:A.G3,2:A.G3,4:A.G3
step#1 pm(>>,forward) area=11.74 rise=3.47 twist=27.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,3:A.G3,2:A.G3,4:A.G3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,3:A.G4,2:A.G4,4:A.G4
step#2 pm(>>,forward) area=8.71 rise=3.15 twist=35.4

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,3:A.G4,2:A.G4,4:A.G4
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,3:A.G5,2:A.G5,4:A.G5
step#3 pm(>>,forward) area=12.54 rise=3.52 twist=25.2

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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 1:A.G2,3:A.G2,2:A.G2,4:A.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,3:A.G3,2:A.G3,4:A.G3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,3:A.G4,2:A.G4,4:A.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,3:A.G5,2:A.G5,4:A.G5
  step#1  pm(>>,forward)  area=11.74 rise=3.47 twist=27.5
  step#2  pm(>>,forward)  area=8.71  rise=3.15 twist=35.4
  step#3  pm(>>,forward)  area=12.54 rise=3.52 twist=25.2
  strand#1  U RNA glyco-bond=---- nts=4 GGGG 1:A.G2,1:A.G3,1:A.G4,1:A.G5
  strand#2  U RNA glyco-bond=---- nts=4 GGGG 3:A.G2,3:A.G3,3:A.G4,3:A.G5
  strand#3  U RNA glyco-bond=---- nts=4 GGGG 2:A.G2,2:A.G3,2:A.G4,2:A.G5
  strand#4  U RNA glyco-bond=---- nts=4 GGGG 4:A.G2,4:A.G3,4:A.G4,4: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)