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

PDB-id
5v3f
Class
RNA
Method
X-ray (1.7 Å)
Summary
Co-crystal structure of the fluorogenic RNA mango
Reference
Trachman, R.J., Demeshkina, N.A., Lau, M.W.L., Panchapakesan, S.S.S., Jeng, S.C.Y., Unrau, P.J., Ferre-D'Amare, A.R.: (2017) "Structural basis for high-affinity fluorophore binding and activation by RNA Mango." Nat. Chem. Biol., 13, 807-813.
Abstract
Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (Kd ∼3 nM), and, in complex with related ligands, it is one of the most redshifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7-Å-resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and form a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization.
G4 notes
6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 3(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

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

 1 glyco-bond=---- groove=---- planarity=0.339 type=bowl-2 nts=4 GGGG A.G8,A.G13,A.G18,A.G23
 2 glyco-bond=---- groove=---- planarity=0.185 type=saddle nts=4 GGGG A.G9,A.G14,A.G19,A.G24
 3 glyco-bond=s--- groove=w--n planarity=0.283 type=other  nts=4 GGGG A.G10,A.G16,A.G21,A.G26
 4 glyco-bond=---- groove=---- planarity=0.349 type=bowl-2 nts=4 GGGG B.G8,B.G13,B.G18,B.G23
 5 glyco-bond=---- groove=---- planarity=0.182 type=saddle nts=4 GGGG B.G9,B.G14,B.G19,B.G24
 6 glyco-bond=s--- groove=w--n planarity=0.283 type=other  nts=4 GGGG B.G10,B.G16,B.G21,B.G26

List of 1 G4-helix [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, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.G10,A.G16,A.G21,A.G26
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G13,B.G8,B.G23,B.G18
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G14,B.G9,B.G24,B.G19
 6  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG B.G16,B.G10,B.G26,B.G21
  step#1  pp(><,inward)   area=26.53 rise=3.42 twist=28.5
  step#2  mp(<<,backward) area=8.06  rise=3.26 twist=34.3
  step#3  mm(<>,outward)  area=24.36 rise=3.59 twist=0.3
  step#4  pm(>>,forward)  area=8.59  rise=3.28 twist=34.0
  step#5  pp(><,inward)   area=27.13 rise=3.43 twist=27.8
  strand#1 RNA glyco-bond=s----- nts=6 GGGGGG A.G10,A.G9,A.G8,B.G13,B.G14,B.G16
  strand#2 RNA glyco-bond=-----s nts=6 GGGGGG A.G16,A.G14,A.G13,B.G8,B.G9,B.G10
  strand#3 RNA glyco-bond=------ nts=6 GGGGGG A.G21,A.G19,A.G18,B.G23,B.G24,B.G26
  strand#4 RNA glyco-bond=------ nts=6 GGGGGG A.G26,A.G24,A.G23,B.G18,B.G19,B.G21

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5 stacking diagrams
 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.G10,A.G16,A.G21,A.G26
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24
step#1 pp(><,inward) area=26.53 rise=3.42 twist=28.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23
step#2 mp(<<,backward) area=8.06 rise=3.26 twist=34.3

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G13,B.G8,B.G23,B.G18
step#3 mm(<>,outward) area=24.36 rise=3.59 twist=0.3

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G13,B.G8,B.G23,B.G18
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G14,B.G9,B.G24,B.G19
step#4 pm(>>,forward) area=8.59 rise=3.28 twist=34.0

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G14,B.G9,B.G24,B.G19
6 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG B.G16,B.G10,B.G26,B.G21
step#5 pp(><,inward) area=27.13 rise=3.43 twist=27.8

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.G10,A.G16,A.G21,A.G26
  step#1  pm(>>,forward)  area=8.06  rise=3.26 twist=34.3
  step#2  pp(><,inward)   area=26.53 rise=3.42 twist=28.5
  strand#1  U RNA glyco-bond=--s nts=3 GGG A.G8,A.G9,A.G10
  strand#2* U RNA glyco-bond=--- nts=3 GGG A.G13,A.G14,A.G16 bulged-nts=1 U A.U15
  strand#3* U RNA glyco-bond=--- nts=3 GGG A.G18,A.G19,A.G21 bulged-nts=1 A A.A20
  strand#4* U RNA glyco-bond=--- nts=3 GGG A.G23,A.G24,A.G26 bulged-nts=1 A A.A25
  loop#1 type=propeller strands=[#1,#2] nts=2 AC A.A11,A.C12
  loop#2 type=propeller strands=[#2,#3] nts=1 C A.C17
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.A22

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G9,B.G14,B.G19,B.G24
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG B.G10,B.G16,B.G21,B.G26
  step#1  pm(>>,forward)  area=8.59  rise=3.28 twist=34.0
  step#2  pp(><,inward)   area=27.13 rise=3.43 twist=27.8
  strand#1  U RNA glyco-bond=--s nts=3 GGG B.G8,B.G9,B.G10
  strand#2* U RNA glyco-bond=--- nts=3 GGG B.G13,B.G14,B.G16 bulged-nts=1 U B.U15
  strand#3* U RNA glyco-bond=--- nts=3 GGG B.G18,B.G19,B.G21 bulged-nts=1 A B.A20
  strand#4* U RNA glyco-bond=--- nts=3 GGG B.G23,B.G24,B.G26 bulged-nts=1 A B.A25
  loop#1 type=propeller strands=[#1,#2] nts=2 AC B.A11,B.C12
  loop#2 type=propeller strands=[#2,#3] nts=1 C B.C17
  loop#3 type=propeller strands=[#3,#4] nts=1 A B.A22

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

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