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

PDB-id
3ibk
Class
RNA
Method
X-ray (2.2 Å)
Summary
Crystal structure of a telomeric RNA quadruplex
Reference
Collie, G.W., Haider, S.M., Neidle, S., Parkinson, G.N.: (2010) "A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex." Nucleic Acids Res., 38, 5569-5580.
Abstract
DNA telomeric repeats in mammalian cells are transcribed to guanine-rich RNA sequences, which adopt parallel-stranded G-quadruplexes with a propeller-like fold. The successful crystallization and structure analysis of a bimolecular human telomeric RNA G-quadruplex, folded into the same crystalline environment as an equivalent DNA oligonucleotide sequence, is reported here. The structural basis of the increased stability of RNA telomeric quadruplexes over DNA ones and their preference for parallel topologies is described here. Our findings suggest that the 2'-OH hydroxyl groups in the RNA quadruplex play a significant role in redefining hydration structure in the grooves and the hydrogen bonding networks. The preference for specific nucleotides to populate the C3'-endo sugar pucker domain is accommodated by alterations in the phosphate backbone, which leads to greater stability through enhanced hydrogen bonding networks. Molecular dynamics simulations on the DNA and RNA quadruplexes are consistent with these findings. The computations, based on the native crystal structure, provide an explanation for RNA G-quadruplex ligand binding selectivity for a group of naphthalene diimide ligands as compared to the DNA G-quadruplex.
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=0.167 type=other  nts=4 GGGG A.G3,A.G9,B.G15,B.G21
 2 glyco-bond=---- groove=---- planarity=0.100 type=planar nts=4 GGGG A.G4,A.G10,B.G16,B.G22
 3 glyco-bond=---- groove=---- planarity=0.288 type=bowl   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=8.91  rise=3.21 twist=34.2
  step#2  pm(>>,forward)  area=13.77 rise=3.60 twist=24.9
  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=8.91 rise=3.21 twist=34.2

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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=13.77 rise=3.60 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, 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=8.91  rise=3.21 twist=34.2
  step#2  pm(>>,forward)  area=13.77 rise=3.60 twist=24.9
  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)