DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 6e80
Class: RNA
Method: X-ray (2.901 Å)
Summary: Crystal structure of the corn aptamer in unliganded state
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: 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 2(-P-P-P), coaxial interfaces: 5'/5'

Cartoon-block schematics in six views (download the tarball)

List of 4 G-tetrads

 1 glyco-bond=---- sugar=-333 groove=---- planarity=0.216 type=other  O+ nts=4 GGGG 1:A.G12,1:A.G15,1:A.G22,1:A.G25
 2 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.227 type=other  O+ nts=4 GGGG 1:A.G13,1:A.G16,1:A.G23,1:A.G26
 3 glyco-bond=---- sugar=-333 groove=---- planarity=0.216 type=other  O+ nts=4 GGGG 2:A.G12,2:A.G15,2:A.G22,2:A.G25
 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.227 type=other  O+ nts=4 GGGG 2:A.G13,2:A.G16,2:A.G23,2: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, 4 G-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G13,1:A.G16,1:A.G23,1:A.G26 2* glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G12,1:A.G15,1:A.G22,1:A.G25 3 glyco-bond=---- sugar=33-3 groove=---- Major-->WC O+ nts=4 GGGG 2:A.G22,2:A.G15,2:A.G12,2:A.G25 4 glyco-bond=---- sugar=-3-3 groove=---- Major-->WC O+ nts=4 GGGG 2:A.G23,2:A.G16,2:A.G13,2:A.G26 step#1 mp(<<,backward) area=9.92 rise=3.19 twist=34.3 step#2 mm(<>,outward) area=14.62 rise=3.43 twist=23.8 step#3 pm(>>,forward) area=9.92 rise=3.19 twist=34.3 strand#1 RNA glyco-bond=---- sugar=--3- nts=4 GGGG 1:A.G13,1:A.G12,2:A.G22,2:A.G23 strand#2 RNA glyco-bond=---- sugar=3333 nts=4 GGGG 1:A.G16,1:A.G15,2:A.G15,2:A.G16 strand#3 RNA glyco-bond=---- sugar=-3-- nts=4 GGGG 1:A.G23,1:A.G22,2:A.G12,2:A.G13 strand#4 RNA glyco-bond=---- sugar=3333 nts=4 GGGG 1:A.G26,1:A.G25,2:A.G25,2:A.G26 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G13,1:A.G16,1:A.G23,1:A.G26 2* glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G12,1:A.G15,1:A.G22,1:A.G25 step#1 mp(<<,backward) area=9.92 rise=3.19 twist=34.3 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G12,1:A.G15,1:A.G22,1:A.G25 3 glyco-bond=---- sugar=33-3 groove=---- Major-->WC O+ nts=4 GGGG 2:A.G22,2:A.G15,2:A.G12,2:A.G25 step#2 mm(<>,outward) area=14.62 rise=3.43 twist=23.8 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=33-3 groove=---- Major-->WC O+ nts=4 GGGG 2:A.G22,2:A.G15,2:A.G12,2:A.G25 4 glyco-bond=---- sugar=-3-3 groove=---- Major-->WC O+ nts=4 GGGG 2:A.G23,2:A.G16,2:A.G13,2:A.G26 step#3 pm(>>,forward) area=9.92 rise=3.19 twist=34.3 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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 1:A.G12,1:A.G15,1:A.G22,1:A.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G13,1:A.G16,1:A.G23,1:A.G26
  step#1  pm(>>,forward)  area=9.92  rise=3.19 twist=34.3
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG 1:A.G12,1:A.G13
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G15,1:A.G16
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG 1:A.G22,1:A.G23
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G25,1:A.G26
  loop#1 type=propeller strands=[#1,#2] nts=1 A 1:A.A14
  loop#2 type=propeller strands=[#2,#3] nts=5 UCUGA 1:A.U17,1:A.C18,1:A.U19,1:A.G20,1:A.A21
  loop#3 type=propeller strands=[#3,#4] nts=1 A 1:A.A24

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 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 2:A.G12,2:A.G15,2:A.G22,2:A.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 2:A.G13,2:A.G16,2:A.G23,2:A.G26
  step#1  pm(>>,forward)  area=9.92  rise=3.19 twist=34.3
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG 2:A.G12,2:A.G13
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG 2:A.G15,2:A.G16
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG 2:A.G22,2:A.G23
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG 2:A.G25,2:A.G26
  loop#1 type=propeller strands=[#1,#2] nts=1 A 2:A.A14
  loop#2 type=propeller strands=[#2,#3] nts=5 UCUGA 2:A.U17,2:A.C18,2:A.U19,2:A.G20,2:A.A21
  loop#3 type=propeller strands=[#3,#4] nts=1 A 2:A.A24