DSSR-enabled G4 identification/annotation: PDB entry 1mdg
Summary information and primary citation
- PDB-id
- 1mdg
- Class
- RNA
- Method
- X-ray (1.5 Å)
- Summary
- An alternating antiparallel octaplex in an RNA crystal structure
- Reference
- Pan BC, Xiong Y, Shi K, Sundaralingam M (2003): "An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction." Structure, 11, 825-831. doi: 10.1016/S0969-2126(03)00108-4.
- 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, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.110 type=planar -- nts=4 gggg 1:A.BGM2,4:A.BGM2,2:A.BGM2,3:A.BGM2 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.171 type=other -- nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 3 glyco-bond=---- sugar=3333 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
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-tetrads, inter-molecular, with 1 stem
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 gggg 1:A.BGM2,4:A.BGM2,2:A.BGM2,3:A.BGM2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 3 glyco-bond=---- sugar=3333 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=--- sugar=-33 nts=3 gGG 1:A.BGM2,1:A.G4,1:A.G5 strand#2 RNA glyco-bond=--- sugar=-33 nts=3 gGG 4:A.BGM2,4:A.G4,4:A.G5 strand#3 RNA glyco-bond=--- sugar=-33 nts=3 gGG 2:A.BGM2,2:A.G4,2:A.G5 strand#4 RNA glyco-bond=--- sugar=-33 nts=3 gGG 3:A.BGM2,3:A.G4,3:A.G5 |
| 2 stacking diagrams | |
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 gggg 1:A.BGM2,4:A.BGM2,2:A.BGM2,3:A.BGM2 |
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2 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 |
List of 1 G4-stem
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-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 gggg 1:A.BGM2,4:A.BGM2,2:A.BGM2,3:A.BGM2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4 3 glyco-bond=---- sugar=3333 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* U RNA glyco-bond=--- sugar=-33 nts=3 gGG 1:A.BGM2,1:A.G4,1:A.G5 bulged-nts=1 A 1:A.A3 strand#2* U RNA glyco-bond=--- sugar=-33 nts=3 gGG 4:A.BGM2,4:A.G4,4:A.G5 bulged-nts=1 A 4:A.A3 strand#3* U RNA glyco-bond=--- sugar=-33 nts=3 gGG 2:A.BGM2,2:A.G4,2:A.G5 bulged-nts=1 A 2:A.A3 strand#4* U RNA glyco-bond=--- sugar=-33 nts=3 gGG 3:A.BGM2,3:A.G4,3:A.G5 bulged-nts=1 A 3:A.A3 |