Summary information

PDB id
6pq7
Class
RNA
Method
X-ray (3.0 Å)
Summary
Structure of the imango-iii fluorescent aptamer at room temperature.
Reference
Trachman III RJ, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferre-D'Amare AR (2019): "Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser." Acta Crystallogr.,Sect.F, 75, 547-551. doi: 10.1107/S2053230X19010136.
Abstract
Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III-TO1-biotin co-crystal structure has now been determined at 3.0 Å resolution. This structural model, which was refined against a data set of ∼1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump-probe experiments on fluorescent RNA-small molecule complexes.
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

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List of 2 G-tetrads

 1 glyco-bond=---s sugar=-33- groove=--wn planarity=0.350 type=other  nts=4 GGGG C.G8,C.G12,C.G17,C.G24
 2 glyco-bond=---s sugar=-3-3 groove=--wn planarity=0.262 type=other  nts=4 GGGG C.G9,C.G13,C.G18,C.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 C.G8,C.G12,C.G17,C.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G22
  step#1  pm(>>,forward)  area=9.08  rise=3.51 twist=31.1
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG C.G8,C.G9
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG C.G12,C.G13
  strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG C.G17,C.G18
  strand#4 RNA glyco-bond=ss sugar=-3 nts=2 GG C.G24,C.G22

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1 stacking diagram 
 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG C.G8,C.G12,C.G17,C.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G22
  step#1  pm(>>,forward)  area=9.08  rise=3.51 twist=31.1

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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 C.G8,C.G12,C.G17,C.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G22
  step#1  pm(>>,forward)  area=9.08  rise=3.51 twist=31.1
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG C.G8,C.G9
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG C.G12,C.G13
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG C.G17,C.G18
  strand#4* D RNA glyco-bond=ss sugar=-3 nts=2 GG C.G24,C.G22 bulged-nts=1 G C.G23
  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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