Summary information [schematics · tetrads · helices · stems · costacks · homepage]

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, R.J., Cojocaru, R., Wu, D., Piszczek, G., Ryckelynck, M., Unrau, P.J., Ferre-D'Amare, A.R.: (2020) "Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair." Structure, 28, 776-785.e3.
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 [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

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

List of 2 G4-helices [summary · schematics · tetrads · stems · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG B.G7,B.G12,B.G17,B.G23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24
 3  glyco-bond=---- groove=---- Major-->WC 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=--- nts=3 GGG B.G7,B.G8,B.G10
  strand#2 RNA glyco-bond=--- nts=3 GGG B.G12,B.G13,B.G15
  strand#3 RNA glyco-bond=--- nts=3 GGG B.G17,B.G18,B.G21
  strand#4 RNA glyco-bond=--- nts=3 GGG B.G23,B.G24,B.G26

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G7,B.G12,B.G17,B.G23
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24
step#1 pm(>>,forward) area=10.15 rise=3.53 twist=31.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G10,B.G15,B.G21,B.G26
step#2 pp(><,inward) area=27.71 rise=3.36 twist=25.2

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.G7,D.G12,D.G17,D.G23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.G8,D.G13,D.G18,D.G24
 3  glyco-bond=---- groove=---- Major-->WC 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=--- nts=3 GGG D.G7,D.G8,D.G10
  strand#2 RNA glyco-bond=--- nts=3 GGG D.G12,D.G13,D.G15
  strand#3 RNA glyco-bond=--- nts=3 GGG D.G17,D.G18,D.G21
  strand#4 RNA glyco-bond=--- nts=3 GGG D.G23,D.G24,D.G26

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.G7,D.G12,D.G17,D.G23
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.G8,D.G13,D.G18,D.G24
step#1 pm(>>,forward) area=10.12 rise=3.46 twist=30.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.G8,D.G13,D.G18,D.G24
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G10,D.G15,D.G21,D.G26
step#2 pp(><,inward) area=27.80 rise=3.40 twist=25.6

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List of 2 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG B.G7,B.G12,B.G17,B.G23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G24
  step#1  pm(>>,forward)  area=10.15 rise=3.53 twist=31.5
  strand#1  U RNA glyco-bond=-- nts=2 GG B.G7,B.G8
  strand#2  U RNA glyco-bond=-- nts=2 GG B.G12,B.G13
  strand#3  U RNA glyco-bond=-- nts=2 GG B.G17,B.G18
  strand#4  U RNA glyco-bond=-- 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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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.G7,D.G12,D.G17,D.G23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG D.G8,D.G13,D.G18,D.G24
  step#1  pm(>>,forward)  area=10.12 rise=3.46 twist=30.8
  strand#1  U RNA glyco-bond=-- nts=2 GG D.G7,D.G8
  strand#2  U RNA glyco-bond=-- nts=2 GG D.G12,D.G13
  strand#3  U RNA glyco-bond=-- nts=2 GG D.G17,D.G18
  strand#4  U RNA glyco-bond=-- nts=2 GG D.G23,D.G24
  loop#1 type=propeller strands=[#1,#2] nts=3 AGU D.A9,D.G10,D.U11
  loop#2 type=propeller strands=[#2,#3] nts=3 UGA D.U14,D.G15,D.A16
  loop#3 type=propeller strands=[#3,#4] nts=4 AUGA D.A19,D.U20,D.G21,D.A22

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)