DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 6v9b
Class: RNA
Method: X-ray (2.4 Å)
Summary: Co-crystal structure of the fluorogenic mango-iv homodimer bound to to1-biotin
Reference: Trachman 3rd RJ, Cojocaru R, Wu D, Piszczek G, Ryckelynck M, Unrau PJ, Ferre-D'Amare AR (2020): "Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair." Structure, 28, 776-785.e3. doi: 10.1016/j.str.2020.04.007.
Abstract: Fluorescent RNA aptamers have been used in cells as biosensor reporters and tags for tracking transcripts. Recently, combined SELEX and microfluidic fluorescence sorting yielded three aptamers that activate fluorescence of TO1-Biotin: Mango-II, Mango-III, and Mango-IV. Of these, Mango-IV was best at imaging RNAs in both fixed and live mammalian cells. To understand how Mango-IV achieves activity in cells, we determined its crystal structure complexed with TO1-Biotin. The structure reveals a domain-swapped homodimer with two independent G-quadruplex fluorophore binding pockets. Structure-based analyses indicate that the Mango-IV core has relaxed fluorophore specificity, and a tendency to reorganize binding pocket residues. These molecular properties may endow it with robustness in the cellular milieu. Based on the domain-swapped structure, heterodimers between Mango-IV and the fluorescent aptamer iSpinach, joined by Watson-Crick base pairing, were constructed. These exhibited FRET between their respective aptamer-activated fluorophores, advancing fluorescent aptamer technology toward multi-color, RNA-based imaging of RNA coexpression and colocalization.
G4 notes: 6 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0, 3(-P-P-P)

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

List of 6 G-tetrads

 1 glyco-bond=---- sugar=3333 groove=---- planarity=0.280 type=other  O+ nts=4 GGGG B.G7,B.G12,B.G17,B.G23
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.145 type=planar O+ nts=4 GGGG B.G8,B.G13,B.G18,B.G24
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.162 type=other  O- nts=4 GGGG B.G10,B.G26,B.G21,B.G15
 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.238 type=other  O+ nts=4 GGGG D.G7,D.G12,D.G17,D.G23
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.155 type=planar O+ nts=4 GGGG D.G8,D.G13,D.G18,D.G24
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.181 type=other  O- nts=4 GGGG D.G10,D.G26,D.G21,D.G15

List of 2 G4-helices

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, INTRA-molecular, with 1 stem

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G7,B.G12,B.G17,B.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G8,B.G13,B.G18,B.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG B.G10,B.G15,B.G21,B.G26 step#1 pm(>>,forward) area=10.15 rise=3.53 twist=31.5 step#2 pp(><,inward) area=27.71 rise=3.36 twist=25.2 strand#1 RNA glyco-bond=--- sugar=33- nts=3 GGG B.G7,B.G8,B.G10 strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG B.G12,B.G13,B.G15 strand#3 RNA glyco-bond=--- sugar=33- nts=3 GGG B.G17,B.G18,B.G21 strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG B.G23,B.G24,B.G26 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G7,B.G12,B.G17,B.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G8,B.G13,B.G18,B.G24 step#1 pm(>>,forward) area=10.15 rise=3.53 twist=31.5 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G8,B.G13,B.G18,B.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG B.G10,B.G15,B.G21,B.G26 step#2 pp(><,inward) area=27.71 rise=3.36 twist=25.2 Download PDB file Interactive view in 3Dmol.js

Helix#2, 3 G-tetrads, INTRA-molecular, with 1 stem

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG D.G7,D.G12,D.G17,D.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG D.G8,D.G13,D.G18,D.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG D.G10,D.G15,D.G21,D.G26 step#1 pm(>>,forward) area=10.12 rise=3.46 twist=30.8 step#2 pp(><,inward) area=27.80 rise=3.40 twist=25.6 strand#1 RNA glyco-bond=--- sugar=33- nts=3 GGG D.G7,D.G8,D.G10 strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG D.G12,D.G13,D.G15 strand#3 RNA glyco-bond=--- sugar=33- nts=3 GGG D.G17,D.G18,D.G21 strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG D.G23,D.G24,D.G26 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG D.G7,D.G12,D.G17,D.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG D.G8,D.G13,D.G18,D.G24 step#1 pm(>>,forward) area=10.12 rise=3.46 twist=30.8 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG D.G8,D.G13,D.G18,D.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG D.G10,D.G15,D.G21,D.G26 step#2 pp(><,inward) area=27.80 rise=3.40 twist=25.6 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, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G7,B.G12,B.G17,B.G23
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G8,B.G13,B.G18,B.G24
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG B.G10,B.G15,B.G21,B.G26
  step#1  pm(>>,forward)  area=10.15 rise=3.53 twist=31.5
  step#2  pp(><,inward)   area=27.71 rise=3.36 twist=25.2
  strand#1* U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G7,B.G8,B.G10 bulged-nts=1 A B.A9
  strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G12,B.G13,B.G15 bulged-nts=1 U B.U14
  strand#3* U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G17,B.G18,B.G21 bulged-nts=2 AU B.A19,B.U20
  strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G23,B.G24,B.G26 bulged-nts=1 C B.C25
  loop#1 type=propeller strands=[#1,#2] nts=1 U B.U11
  loop#2 type=propeller strands=[#2,#3] nts=1 A B.A16
  loop#3 type=propeller strands=[#3,#4] nts=1 A B.A22

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG D.G7,D.G12,D.G17,D.G23
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG D.G8,D.G13,D.G18,D.G24
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG D.G10,D.G15,D.G21,D.G26
  step#1  pm(>>,forward)  area=10.12 rise=3.46 twist=30.8
  step#2  pp(><,inward)   area=27.80 rise=3.40 twist=25.6
  strand#1* U RNA glyco-bond=--- sugar=33- nts=3 GGG D.G7,D.G8,D.G10 bulged-nts=1 A D.A9
  strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG D.G12,D.G13,D.G15 bulged-nts=1 U D.U14
  strand#3* U RNA glyco-bond=--- sugar=33- nts=3 GGG D.G17,D.G18,D.G21 bulged-nts=2 AU D.A19,D.U20
  strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG D.G23,D.G24,D.G26 bulged-nts=1 C D.C25
  loop#1 type=propeller strands=[#1,#2] nts=1 U D.U11
  loop#2 type=propeller strands=[#2,#3] nts=1 A D.A16
  loop#3 type=propeller strands=[#3,#4] nts=1 A D.A22