DSSR-enabled G4 identification/annotation: PDB entry 6e82
Summary information and primary citation
- PDB-id
- 6e82
- Class
- RNA
- Method
- X-ray (3.101 Å)
- Summary
- Crystal structure of the corn aptamer mutant a14u in complex with tht
- Reference
- Sjekloca L, Ferre-D'Amare AR (2019): "Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence." Cell Chem Biol, 26, 1159. doi: 10.1016/j.chembiol.2019.04.012.
- Abstract
- Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 2 G-tetrads
1 glyco-bond=---- sugar=-333 groove=---- planarity=0.396 type=other O+ nts=4 GGGG A.G12,A.G15,A.G22,A.G25 2 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.469 type=other O+ nts=4 UGGG A.U14,A.G16,A.G23,A.G26
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
|
1 glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG A.G12,A.G15,A.G22,A.G25 2 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 UGGG A.U14,A.G16,A.G23,A.G26 step#1 pm(>>,forward) area=10.96 rise=3.28 twist=37.9 strand#1 RNA glyco-bond=-- sugar=-- nts=2 GU A.G12,A.U14 strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG A.G15,A.G16 strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG A.G22,A.G23 strand#4 RNA glyco-bond=-- sugar=33 nts=2 GG A.G25,A.G26 |
| 1 stacking diagram | |
|
1 glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG A.G12,A.G15,A.G22,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, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG A.G12,A.G15,A.G22,A.G25 2 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 UGGG A.U14,A.G16,A.G23,A.G26 step#1 pm(>>,forward) area=10.96 rise=3.28 twist=37.9 strand#1* U RNA glyco-bond=-- sugar=-- nts=2 GU A.G12,A.U14 bulged-nts=1 G A.G13 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG A.G15,A.G16 strand#3 U RNA glyco-bond=-- sugar=3- nts=2 GG A.G22,A.G23 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG A.G25,A.G26 loop#1 type=propeller strands=[#1,#2] nts=0 loop#2 type=propeller strands=[#2,#3] nts=5 UCUGA A.U17,A.C18,A.U19,A.G20,A.A21 loop#3 type=propeller strands=[#3,#4] nts=1 A A.A24 |