Summary information

PDB id
6e8u
Class
RNA
Method
X-ray (1.55 Å)
Summary
Structure of the mango-iii (a10u) aptamer bound to to1-biotin
Reference
Trachman 3rd RJ, Autour A, Jeng SCY, Abdolahzadeh A, Andreoni A, Cojocaru R, Garipov R, Dolgosheina EV, Knutson JR, Ryckelynck M, Unrau PJ, Ferre-D'Amare AR (2019): "Structure and functional reselection of the Mango-III fluorogenic RNA aptamer." Nat. Chem. Biol., 15, 472-479. doi: 10.1038/s41589-019-0267-9.
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
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-Lw), hybrid-2R(3+1), UUUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=---s sugar=-33- groove=--wn planarity=0.321 type=other  nts=4 GGGG B.G8,B.G12,B.G17,B.G24
 2 glyco-bond=---s sugar=-3-3 groove=--wn planarity=0.260 type=other  nts=4 GGGG B.G9,B.G13,B.G18,B.G22

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

 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG B.G8,B.G12,B.G17,B.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG B.G9,B.G13,B.G18,B.G22
  step#1  pm(>>,forward)  area=8.76  rise=3.42 twist=31.1
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG B.G8,B.G9
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG B.G12,B.G13
  strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG B.G17,B.G18
  strand#4 RNA glyco-bond=ss sugar=-3 nts=2 GG B.G24,B.G22

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG B.G8,B.G12,B.G17,B.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG B.G9,B.G13,B.G18,B.G22
  step#1  pm(>>,forward)  area=8.76  rise=3.42 twist=31.1

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4-stem

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, UUUD, hybrid-(mixed), 2(-P-P-Lw), hybrid-2R(3+1)

 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG B.G8,B.G12,B.G17,B.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG B.G9,B.G13,B.G18,B.G22
  step#1  pm(>>,forward)  area=8.76  rise=3.42 twist=31.1
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG B.G8,B.G9
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG B.G12,B.G13
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG B.G17,B.G18
  strand#4* D RNA glyco-bond=ss sugar=-3 nts=2 GG B.G24,B.G22 bulged-nts=1 G B.G23
  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

Download PDB file
Interactive view in 3Dmol.js