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

PDB-id
2kbp
Class
RNA
Method
NMR
Summary
Solution structure of a G-quadruplex of human telomeric RNA
Reference
Martadinata, H., Phan, A.T.: (2009) "Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution." J.Am.Chem.Soc., 131, 2570-2578.
Abstract
Very recent studies showed that mammalian telomeres were transcribed into telomeric-repeat-containing RNAs and suggested that these RNA molecules were biologically important. Here we report on a structural study of RNA G-quadruplexes formed by human telomeric RNA sequences in K(+) solution. Our data indicated that these sequences formed propeller-type parallel-stranded RNA G-quadruplexes. We have determined the NMR-based solution structure of a dimeric propeller-type RNA G-quadruplex formed by the 12-nt human telomeric RNA sequence r(UAGGGUUAGGGU). We also observed the stacking of two such propeller-type G-quadruplex blocks for the 10-nt human telomeric RNA sequence r(GGGUUAGGGU) and a higher-order G-quadruplex structure for the 9-nt human telomeric RNA sequence r(GGGUUAGGG). Based on these findings we proposed how higher-order structures might be formed by long telomeric RNA.
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]

PyMOL session file PDB file View in 3Dmol.js

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

 1 glyco-bond=---- groove=---- planarity=0.234 type=other  nts=4 GGGG A.G3,A.G9,B.G15,B.G21
 2 glyco-bond=---- groove=---- planarity=0.169 type=other  nts=4 GGGG A.G4,A.G10,B.G16,B.G22
 3 glyco-bond=---- groove=---- planarity=0.246 type=other  nts=4 GGGG A.G5,A.G11,B.G17,B.G23

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 A.G3,A.G9,B.G15,B.G21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,A.G10,B.G16,B.G22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,A.G11,B.G17,B.G23
  step#1  pm(>>,forward)  area=8.17  rise=3.71 twist=33.8
  step#2  pm(>>,forward)  area=14.42 rise=4.29 twist=26.5
  strand#1 RNA glyco-bond=--- nts=3 GGG A.G3,A.G4,A.G5
  strand#2 RNA glyco-bond=--- nts=3 GGG A.G9,A.G10,A.G11
  strand#3 RNA glyco-bond=--- nts=3 GGG B.G15,B.G16,B.G17
  strand#4 RNA glyco-bond=--- nts=3 GGG B.G21,B.G22,B.G23

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G15,B.G21
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,A.G10,B.G16,B.G22
step#1 pm(>>,forward) area=8.17 rise=3.71 twist=33.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,A.G10,B.G16,B.G22
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,A.G11,B.G17,B.G23
step#2 pm(>>,forward) area=14.42 rise=4.29 twist=26.5

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G15,B.G21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,A.G10,B.G16,B.G22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,A.G11,B.G17,B.G23
  step#1  pm(>>,forward)  area=8.17  rise=3.71 twist=33.8
  step#2  pm(>>,forward)  area=14.42 rise=4.29 twist=26.5
  strand#1  U RNA glyco-bond=--- nts=3 GGG A.G3,A.G4,A.G5
  strand#2  U RNA glyco-bond=--- nts=3 GGG A.G9,A.G10,A.G11
  strand#3  U RNA glyco-bond=--- nts=3 GGG B.G15,B.G16,B.G17
  strand#4  U RNA glyco-bond=--- nts=3 GGG B.G21,B.G22,B.G23
  loop#1 type=propeller strands=[#1,#2] nts=3 UUA A.U6,A.U7,A.A8
  loop#2 type=propeller strands=[#3,#4] nts=3 UUA B.U18,B.U19,B.A20

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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)