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

PDB-id
6e8t
Class
RNA
Method
X-ray (2.9 Å)
Summary
Structure of the mango-iii (a10u) aptamer bound to to1-biotin
Reference
Trachman 3rd., R.J., Autour, A., Jeng, S.C.Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov, R., Dolgosheina, E.V., Knutson, J.R., Ryckelynck, M., Unrau, P.J., Ferre-D'Amare, A.R.: (2019) "Structure and functional reselection of the Mango-III fluorogenic RNA aptamer." Nat. Chem. Biol., 15, 472-479.
Abstract
Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.
G4 notes
8 G-tetrads, 4 G4 helices, 4 G4 stems · 2(-P-Lw), hybrid-1(3+1), UUUD; 2(-P-P-Lw), (3+1), UUUD

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

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List of 8 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---s groove=--wn planarity=0.436 type=other  nts=4 GGGG D.G8,D.G12,D.G17,D.G24
 2 glyco-bond=---s groove=--wn planarity=0.194 type=other  nts=4 GGGG D.G9,D.G13,D.G18,D.G22
 3 glyco-bond=---s groove=--wn planarity=0.426 type=other  nts=4 GGGG C.G8,C.G12,C.G17,C.G24
 4 glyco-bond=---s groove=--wn planarity=0.242 type=other  nts=4 GGGG C.G9,C.G13,C.G18,C.G22
 5 glyco-bond=---s groove=--wn planarity=0.431 type=other  nts=4 GGGG B.G8,B.G12,B.G17,B.G24
 6 glyco-bond=---s groove=--wn planarity=0.201 type=saddle nts=4 GGGG B.G9,B.G13,B.G18,B.G22
 7 glyco-bond=---s groove=--wn planarity=0.382 type=other  nts=4 GGGG A.G8,A.G12,A.G17,A.G24
 8 glyco-bond=---s groove=--wn planarity=0.233 type=other  nts=4 GGGG A.G9,A.G13,A.G18,A.G22

List of 4 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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G8,D.G12,D.G17,D.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G22
  step#1  pm(>>,forward)  area=10.68 rise=3.52 twist=29.1
  strand#1 RNA glyco-bond=-- nts=2 GG D.G8,D.G9
  strand#2 RNA glyco-bond=-- nts=2 GG D.G12,D.G13
  strand#3 RNA glyco-bond=-- nts=2 GG D.G17,D.G18
  strand#4 RNA glyco-bond=ss nts=2 GG D.G24,D.G22

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1 stacking diagram
 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G8,D.G12,D.G17,D.G24
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G22
step#1 pm(>>,forward) area=10.68 rise=3.52 twist=29.1

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

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G8,C.G12,C.G17,C.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G22
  step#1  pm(>>,forward)  area=9.72  rise=3.44 twist=28.6
  strand#1 RNA glyco-bond=-- nts=2 GG C.G8,C.G9
  strand#2 RNA glyco-bond=-- nts=2 GG C.G12,C.G13
  strand#3 RNA glyco-bond=-- nts=2 GG C.G17,C.G18
  strand#4 RNA glyco-bond=ss nts=2 GG C.G24,C.G22

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1 stacking diagram
 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G8,C.G12,C.G17,C.G24
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G22
step#1 pm(>>,forward) area=9.72 rise=3.44 twist=28.6

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

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG B.G8,B.G12,B.G17,B.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG B.G9,B.G13,B.G18,B.G22
  step#1  pm(>>,forward)  area=10.77 rise=3.47 twist=27.5
  strand#1 RNA glyco-bond=-- nts=2 GG B.G8,B.G9
  strand#2 RNA glyco-bond=-- nts=2 GG B.G12,B.G13
  strand#3 RNA glyco-bond=-- nts=2 GG B.G17,B.G18
  strand#4 RNA glyco-bond=ss nts=2 GG B.G24,B.G22

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1 stacking diagram
 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG B.G8,B.G12,B.G17,B.G24
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG B.G9,B.G13,B.G18,B.G22
step#1 pm(>>,forward) area=10.77 rise=3.47 twist=27.5

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Helix#4, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G8,A.G12,A.G17,A.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G9,A.G13,A.G18,A.G22
  step#1  pm(>>,forward)  area=12.03 rise=3.46 twist=28.6
  strand#1 RNA glyco-bond=-- nts=2 GG A.G8,A.G9
  strand#2 RNA glyco-bond=-- nts=2 GG A.G12,A.G13
  strand#3 RNA glyco-bond=-- nts=2 GG A.G17,A.G18
  strand#4 RNA glyco-bond=ss nts=2 GG A.G24,A.G22

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1 stacking diagram
 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G8,A.G12,A.G17,A.G24
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G9,A.G13,A.G18,A.G22
step#1 pm(>>,forward) area=12.03 rise=3.46 twist=28.6

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List of 4 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, 2 loops, INTRA-molecular, UUUD, anti-parallel, 2(-P-Lw), hybrid-1(3+1)

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G8,D.G12,D.G17,D.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G22
  step#1  pm(>>,forward)  area=10.68 rise=3.52 twist=29.1
  strand#1  U RNA glyco-bond=-- nts=2 GG D.G8,D.G9
  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* D RNA glyco-bond=ss nts=2 GG D.G24,D.G22 bulged-nts=1 U D.U23
  loop#1 type=propeller strands=[#2,#3] nts=3 UUU D.U14,D.U15,D.U16
  loop#2 type=lateral   strands=[#3,#4] nts=3 UAU D.U19,D.A20,D.U21

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, anti-parallel, 2(-P-P-Lw), (3+1)

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G8,C.G12,C.G17,C.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G22
  step#1  pm(>>,forward)  area=9.72  rise=3.44 twist=28.6
  strand#1  U RNA glyco-bond=-- nts=2 GG C.G8,C.G9
  strand#2  U RNA glyco-bond=-- nts=2 GG C.G12,C.G13
  strand#3  U RNA glyco-bond=-- nts=2 GG C.G17,C.G18
  strand#4* D RNA glyco-bond=ss nts=2 GG C.G24,C.G22 bulged-nts=1 U C.U23
  loop#1 type=propeller strands=[#1,#2] nts=2 AA C.A10,C.A11
  loop#2 type=propeller strands=[#2,#3] nts=3 UUU C.U14,C.U15,C.U16
  loop#3 type=lateral   strands=[#3,#4] nts=3 UAU C.U19,C.A20,C.U21

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Stem#3, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, anti-parallel, 2(-P-P-Lw), (3+1)

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG B.G8,B.G12,B.G17,B.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG B.G9,B.G13,B.G18,B.G22
  step#1  pm(>>,forward)  area=10.77 rise=3.47 twist=27.5
  strand#1  U RNA glyco-bond=-- nts=2 GG B.G8,B.G9
  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* D RNA glyco-bond=ss nts=2 GG B.G24,B.G22 bulged-nts=1 U B.U23
  loop#1 type=propeller strands=[#1,#2] nts=2 AA B.A10,B.A11
  loop#2 type=propeller strands=[#2,#3] nts=3 UUU B.U14,B.U15,B.U16
  loop#3 type=lateral   strands=[#3,#4] nts=3 UAU B.U19,B.A20,B.U21

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Stem#4, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, anti-parallel, 2(-P-P-Lw), (3+1)

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G8,A.G12,A.G17,A.G24
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.G9,A.G13,A.G18,A.G22
  step#1  pm(>>,forward)  area=12.03 rise=3.46 twist=28.6
  strand#1  U RNA glyco-bond=-- nts=2 GG A.G8,A.G9
  strand#2  U RNA glyco-bond=-- nts=2 GG A.G12,A.G13
  strand#3  U RNA glyco-bond=-- nts=2 GG A.G17,A.G18
  strand#4* D RNA glyco-bond=ss nts=2 GG A.G24,A.G22 bulged-nts=1 U A.U23
  loop#1 type=propeller strands=[#1,#2] nts=2 AA A.A10,A.A11
  loop#2 type=propeller strands=[#2,#3] nts=3 UUU A.U14,A.U15,A.U16
  loop#3 type=lateral   strands=[#3,#4] nts=3 UAU A.U19,A.A20,A.U21

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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)