DSSR-curated G4 structure: PDB entry 6v9d

Summary information

PDB id: 6v9d
Class: RNA
Method: X-ray (2.8 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, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=---- sugar=3333 groove=---- planarity=0.300 type=other  nts=4 GGGG B.G7,B.G12,B.G17,B.G23
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.143 type=planar nts=4 GGGG B.G8,B.G13,B.G18,B.G24
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.202 type=other  nts=4 GGGG B.G10,B.G26,B.G21,B.G15
 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.253 type=other  nts=4 GGGG E.G7,E.G12,E.G17,E.G23
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.184 type=other  nts=4 GGGG E.G8,E.G13,E.G18,E.G24
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.202 type=other  nts=4 GGGG E.G10,E.G26,E.G21,E.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-tetrad layers, INTRA-molecular, with 1 stem

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G7,B.G12,B.G17,B.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.G10,B.G15,B.G21,B.G26 step#1 pm(>>,forward) area=8.95 rise=3.44 twist=30.6 step#2 pp(><,inward) area=30.04 rise=3.41 twist=26.2 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 nts=4 GGGG B.G7,B.G12,B.G17,B.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24 step#1 pm(>>,forward) area=8.95 rise=3.44 twist=30.6 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.G10,B.G15,B.G21,B.G26 step#2 pp(><,inward) area=30.04 rise=3.41 twist=26.2 Download PDB file Interactive view in 3Dmol.js

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

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G7,E.G12,E.G17,E.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G8,E.G13,E.G18,E.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG E.G10,E.G15,E.G21,E.G26 step#1 pm(>>,forward) area=9.92 rise=3.45 twist=30.2 step#2 pp(><,inward) area=28.15 rise=3.45 twist=25.8 strand#1 RNA glyco-bond=--- sugar=33- nts=3 GGG E.G7,E.G8,E.G10 strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG E.G12,E.G13,E.G15 strand#3 RNA glyco-bond=--- sugar=33- nts=3 GGG E.G17,E.G18,E.G21 strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG E.G23,E.G24,E.G26 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G7,E.G12,E.G17,E.G23 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G8,E.G13,E.G18,E.G24 step#1 pm(>>,forward) area=9.92 rise=3.45 twist=30.2 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G8,E.G13,E.G18,E.G24 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG E.G10,E.G15,E.G21,E.G26 step#2 pp(><,inward) area=28.15 rise=3.45 twist=25.8 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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G7,B.G12,B.G17,B.G23
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24
  step#1  pm(>>,forward)  area=8.95  rise=3.44 twist=30.6
  strand#1  U RNA glyco-bond=-- sugar=33 nts=2 GG B.G7,B.G8
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG B.G12,B.G13
  strand#3  U RNA glyco-bond=-- sugar=33 nts=2 GG B.G17,B.G18
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG B.G23,B.G24
  loop#1 type=propeller strands=[#1,#2] nts=3 AGU B.A9,B.G10,B.U11
  loop#2 type=propeller strands=[#2,#3] nts=3 UGA B.U14,B.G15,B.A16
  loop#3 type=propeller strands=[#3,#4] nts=4 AUGA B.A19,B.U20,B.G21,B.A22

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Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G7,E.G12,E.G17,E.G23
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.G8,E.G13,E.G18,E.G24
  step#1  pm(>>,forward)  area=9.92  rise=3.45 twist=30.2
  strand#1  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G7,E.G8
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G12,E.G13
  strand#3  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G17,E.G18
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G23,E.G24
  loop#1 type=propeller strands=[#1,#2] nts=3 AGU E.A9,E.G10,E.U11
  loop#2 type=propeller strands=[#2,#3] nts=3 UGA E.U14,E.G15,E.A16
  loop#3 type=propeller strands=[#3,#4] nts=4 AUGA E.A19,E.U20,E.G21,E.A22