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

PDB-id
2grb
Class
RNA
Method
X-ray (1.4 Å)
Summary
Crystal structure of an RNA quadruplex containing inosine-tetrad
Reference
Pan, B., Shi, K., Sundaralingam, M.: (2006) "Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads." J.Mol.Biol., 363, 451-459.
Abstract
Polyinosinic acid has been known to adopt the four-stranded helical structure but its basic unit, inosine tetrad (I tetrad), has not been determined at the atomic level. Here we report the crystal structure of an RNA quadruplex containing an I tetrad at 1.4 A resolution. The I tetrad has one cyclic hydrogen bond N1...O6 with the bond length of 2.7 A. A water bridge is observed in the minor groove side of the base tetrad. Even though it is sandwiched by guanine tetrads (G tetrads), the I tetrad is buckled towards the 3' side of the tetrad plane, which results from the different interaction strength with K ions on two sides of the tetrad plane. Comparison with both G tetrad and adenine tetrad indicates that lack of NH2 in the C2 position makes the I tetrad prone to buckle for interactions with ligands. Two U*(G-G-G-G) base pentads are observed at the junction of the 5' termini of two quadruplexes. The uridine residue in the base pentad is engaged in two hydrogen bonding interactions (N2(G)-H...O2(U) and O2'(G)-H...O4(U)) and a water-mediated interaction (N3(G) and N3(U)) with the G tetrad. We also discuss the roles of amino group in purine tetrads and the inter-quadruplex interactions in RNA molecules. These quadruplexes may interact with each other by stacking, groove binding and intercalation.
G4 notes
8 G-tetrads, 2 G4 helices, 2 G4 stems · parallel(4+0), UUUU

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

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List of 8 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.322 type=other  nts=4 GGGG A.G2,D.G2,B.G2,C.G2
 2 glyco-bond=---- groove=---- planarity=0.327 type=other  nts=4 gggg A.I3,D.I3,B.I3,C.I3
 3 glyco-bond=---- groove=---- planarity=0.175 type=other  nts=4 GGGG A.G4,D.G4,B.G4,C.G4
 4 glyco-bond=---- groove=---- planarity=0.189 type=other  nts=4 GGGG A.G5,D.G5,B.G5,C.G5
 5 glyco-bond=---- groove=---- planarity=0.262 type=other  nts=4 GGGG E.G2,H.G2,F.G2,G.G2
 6 glyco-bond=---- groove=---- planarity=0.279 type=other  nts=4 gggg E.I3,H.I3,F.I3,G.I3
 7 glyco-bond=---- groove=---- planarity=0.140 type=planar nts=4 GGGG E.G4,H.G4,F.G4,G.G4
 8 glyco-bond=---- groove=---- planarity=0.255 type=bowl   nts=4 GGGG E.G5,H.G5,F.G5,G.G5

List of 2 G4-helices [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,D.G2,B.G2,C.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.I3,D.I3,B.I3,C.I3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,D.G4,B.G4,C.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,D.G5,B.G5,C.G5
  step#1  pm(>>,forward)  area=12.12 rise=3.27 twist=32.1
  step#2  pm(>>,forward)  area=6.59  rise=3.48 twist=29.1
  step#3  pm(>>,forward)  area=14.38 rise=3.66 twist=23.6
  strand#1 RNA glyco-bond=---- nts=4 GgGG A.G2,A.I3,A.G4,A.G5
  strand#2 RNA glyco-bond=---- nts=4 GgGG D.G2,D.I3,D.G4,D.G5
  strand#3 RNA glyco-bond=---- nts=4 GgGG B.G2,B.I3,B.G4,B.G5
  strand#4 RNA glyco-bond=---- nts=4 GgGG C.G2,C.I3,C.G4,C.G5

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,D.G2,B.G2,C.G2
2 glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.I3,D.I3,B.I3,C.I3
step#1 pm(>>,forward) area=12.12 rise=3.27 twist=32.1

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.I3,D.I3,B.I3,C.I3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,D.G4,B.G4,C.G4
step#2 pm(>>,forward) area=6.59 rise=3.48 twist=29.1

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,D.G4,B.G4,C.G4
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,D.G5,B.G5,C.G5
step#3 pm(>>,forward) area=14.38 rise=3.66 twist=23.6

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Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G2,H.G2,F.G2,G.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg E.I3,H.I3,F.I3,G.I3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G4,H.G4,F.G4,G.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G5,H.G5,F.G5,G.G5
  step#1  pm(>>,forward)  area=11.61 rise=3.28 twist=32.0
  step#2  pm(>>,forward)  area=6.20  rise=3.50 twist=29.3
  step#3  pm(>>,forward)  area=14.30 rise=3.72 twist=23.3
  strand#1 RNA glyco-bond=---- nts=4 GgGG E.G2,E.I3,E.G4,E.G5
  strand#2 RNA glyco-bond=---- nts=4 GgGG H.G2,H.I3,H.G4,H.G5
  strand#3 RNA glyco-bond=---- nts=4 GgGG F.G2,F.I3,F.G4,F.G5
  strand#4 RNA glyco-bond=---- nts=4 GgGG G.G2,G.I3,G.G4,G.G5

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G2,H.G2,F.G2,G.G2
2 glyco-bond=---- groove=---- WC-->Major nts=4 gggg E.I3,H.I3,F.I3,G.I3
step#1 pm(>>,forward) area=11.61 rise=3.28 twist=32.0

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg E.I3,H.I3,F.I3,G.I3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G4,H.G4,F.G4,G.G4
step#2 pm(>>,forward) area=6.20 rise=3.50 twist=29.3

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G4,H.G4,F.G4,G.G4
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G5,H.G5,F.G5,G.G5
step#3 pm(>>,forward) area=14.30 rise=3.72 twist=23.3

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List of 2 G4-stems [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,D.G2,B.G2,C.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.I3,D.I3,B.I3,C.I3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,D.G4,B.G4,C.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,D.G5,B.G5,C.G5
  step#1  pm(>>,forward)  area=12.12 rise=3.27 twist=32.1
  step#2  pm(>>,forward)  area=6.59  rise=3.48 twist=29.1
  step#3  pm(>>,forward)  area=14.38 rise=3.66 twist=23.6
  strand#1  U RNA glyco-bond=---- nts=4 GgGG A.G2,A.I3,A.G4,A.G5
  strand#2  U RNA glyco-bond=---- nts=4 GgGG D.G2,D.I3,D.G4,D.G5
  strand#3  U RNA glyco-bond=---- nts=4 GgGG B.G2,B.I3,B.G4,B.G5
  strand#4  U RNA glyco-bond=---- nts=4 GgGG C.G2,C.I3,C.G4,C.G5

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G2,H.G2,F.G2,G.G2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg E.I3,H.I3,F.I3,G.I3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G4,H.G4,F.G4,G.G4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.G5,H.G5,F.G5,G.G5
  step#1  pm(>>,forward)  area=11.61 rise=3.28 twist=32.0
  step#2  pm(>>,forward)  area=6.20  rise=3.50 twist=29.3
  step#3  pm(>>,forward)  area=14.30 rise=3.72 twist=23.3
  strand#1  U RNA glyco-bond=---- nts=4 GgGG E.G2,E.I3,E.G4,E.G5
  strand#2  U RNA glyco-bond=---- nts=4 GgGG H.G2,H.I3,H.G4,H.G5
  strand#3  U RNA glyco-bond=---- nts=4 GgGG F.G2,F.I3,F.G4,F.G5
  strand#4  U RNA glyco-bond=---- nts=4 GgGG G.G2,G.I3,G.G4,G.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)