DSSR-enabled G4 identification/annotation: PDB entry 6e8s
Summary information and primary citation
- PDB-id
- 6e8s
- Class
- RNA
- Method
- X-ray (2.35 Å)
- Summary
- Structure of the imango-iii aptamer bound to to1-biotin
- Reference
- Trachman 3rd RJ, Autour A, Jeng SCY, Abdolahzadeh A, Andreoni A, Cojocaru R, Garipov R, Dolgosheina EV, Knutson JR, Ryckelynck M, Unrau PJ, Ferre-D'Amare AR (2019): "Structure and functional reselection of the Mango-III fluorogenic RNA aptamer." Nat. Chem. Biol., 15, 472-479. doi: 10.1038/s41589-019-0267-9.
- Abstract
- Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 2(-P-P-Lw)
Cartoon-block schematics in six views (download the tarball)
List of 2 G-tetrads
1 glyco-bond=---s sugar=-33- groove=--wn planarity=0.480 type=other O+ nts=4 GGGG 1:A.G9,1:A.G13,1:A.G18,1:A.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn planarity=0.294 type=other O+ nts=4 GGGG 1:A.G10,1:A.G14,1:A.G19,1:A.G23
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, 2 G-tetrads, INTRA-molecular, with 1 stem
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1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major O+ nts=4 GGGG 1:A.G9,1:A.G13,1:A.G18,1:A.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G14,1:A.G19,1:A.G23 step#1 pm(>>,forward) area=10.52 rise=3.48 twist=28.7 strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG 1:A.G9,1:A.G10 strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G13,1:A.G14 strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG 1:A.G18,1:A.G19 strand#4 RNA glyco-bond=ss sugar=-3 nts=2 GG 1:A.G25,1:A.G23 |
| 1 stacking diagram | |
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1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major O+ nts=4 GGGG 1:A.G9,1:A.G13,1:A.G18,1:A.G25 |
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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUD, hybrid2, 3+1, 2(-P-P-Lw)
|
1 glyco-bond=---s sugar=-33- groove=--wn WC-->Major O+ nts=4 GGGG 1:A.G9,1:A.G13,1:A.G18,1:A.G25 2 glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G14,1:A.G19,1:A.G23 step#1 pm(>>,forward) area=10.52 rise=3.48 twist=28.7 strand#1 U RNA glyco-bond=-- sugar=-- nts=2 GG 1:A.G9,1:A.G10 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G13,1:A.G14 strand#3 U RNA glyco-bond=-- sugar=3- nts=2 GG 1:A.G18,1:A.G19 strand#4* D RNA glyco-bond=ss sugar=-3 nts=2 GG 1:A.G25,1:A.G23 bulged-nts=1 U 1:A.U24 loop#1 type=propeller strands=[#1,#2] nts=2 AA 1:A.A11,1:A.A12 loop#2 type=propeller strands=[#2,#3] nts=3 AUU 1:A.A15,1:A.U16,1:A.U17 loop#3 type=lateral strands=[#3,#4] nts=3 UAU 1:A.U20,1:A.A21,1:A.U22 |