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

PDB-id
1mdg*
Class
RNA
Method
X-ray (1.5 Å)
Summary
An alternating antiparallel octaplex in an RNA crystal structure
Reference
Pan, B.C., Xiong, Y., Shi, K., Sundaralingam, M.: (2003) "An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction." Structure, 11, 825-831.
Abstract
Multistranded helical structures in nucleic acids play various functions in biological processes. Here we report the crystal structure of a hexamer, rU(BrdG)r(AGGU),at 1.5 A resolution containing a structural complex of an alternating antiparallel eight-stranded helical fragment that is sandwiched in two tetraplexes. The octaplex is formed by groove binding interaction and base tetrad intercalation between two tetraplexes. Two different forms of octaplexes have been proposed, which display different properties in interaction with proteins and nucleic acids. Adenines form a base tetrad in the novel N6-H em leader N3 conformation and further interact with uridines to form an adenine-uridine octad in the reverse Hoogsteen pairing scheme. The conformational flexibility of adenine tetrad indicates that it can optimize its conformation in different interactions.
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=0.110 type=planar nts=4 gggg 1:A.BGM2,4:A.BGM2,2:A.BGM2,3:A.BGM2
 2 glyco-bond=---- groove=---- planarity=0.171 type=other  nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 3 glyco-bond=---- groove=---- planarity=0.230 type=bowl   nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3: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, 3 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg 1:A.BGM2,4:A.BGM2,2:A.BGM2,3:A.BGM2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
  step#1  pm(>>,forward)  area=0.00  rise=6.69 twist=59.2
  step#2  pm(>>,forward)  area=14.27 rise=3.56 twist=23.0
  strand#1 RNA glyco-bond=--- nts=3 gGG 1:A.BGM2,1:A.G4,1:A.G5
  strand#2 RNA glyco-bond=--- nts=3 gGG 4:A.BGM2,4:A.G4,4:A.G5
  strand#3 RNA glyco-bond=--- nts=3 gGG 2:A.BGM2,2:A.G4,2:A.G5
  strand#4 RNA glyco-bond=--- nts=3 gGG 3:A.BGM2,3:A.G4,3:A.G5

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg 1:A.BGM2,4:A.BGM2,2:A.BGM2,3:A.BGM2
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
step#1 pm(>>,forward) area=0.00 rise=6.69 twist=59.2

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
step#2 pm(>>,forward) area=14.27 rise=3.56 twist=23.0

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
  step#1  pm(>>,forward)  area=14.27 rise=3.56 twist=23.0
  strand#1  U RNA glyco-bond=-- nts=2 GG 1:A.G4,1:A.G5
  strand#2  U RNA glyco-bond=-- nts=2 GG 4:A.G4,4:A.G5
  strand#3  U RNA glyco-bond=-- nts=2 GG 2:A.G4,2:A.G5
  strand#4  U RNA glyco-bond=-- nts=2 GG 3:A.G4,3: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)