Summary information

PDB id
5bjo
Class
RNA
Method
X-ray (2.35 Å)
Summary
Crystal structure of the corn RNA aptamer in complex with dfho, site-specific 5-iodo-u
Reference
Warner KD, Sjekloca L, Song W, Filonov GS, Jaffrey SR, Ferre-D'Amare AR (2017): "A homodimer interface without base pairs in an RNA mimic of red fluorescent protein." Nat. Chem. Biol., 13, 1195-1201. doi: 10.1038/nchembio.2475.
Abstract
Corn, a 28-nucleotide RNA, increases yellow fluorescence of its cognate ligand 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO) by >400-fold. Corn was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, in which six unpaired adenosines break overall two-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its interprotomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could provide a basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful for analyzing RNA co-expression or association, or for designing self-assembling RNA nanostructures.
G4 notes
4 G-tetrads, 2 G4 helices, 2 G4 stems, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=-333 groove=---- planarity=0.341 type=other  nts=4 GGGG E.G12,E.G15,E.G22,E.G25
 2 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.205 type=other  nts=4 GGGG E.G13,E.G16,E.G23,E.G26
 3 glyco-bond=---- sugar=-333 groove=---- planarity=0.360 type=other  nts=4 GGGG Y.G12,Y.G15,Y.G22,Y.G25
 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.273 type=other  nts=4 GGGG Y.G13,Y.G16,Y.G23,Y.G26

List of 2 G4-helices

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=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG E.G12,E.G15,E.G22,E.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG E.G13,E.G16,E.G23,E.G26
  step#1  pm(>>,forward)  area=10.56 rise=3.38 twist=32.5
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG E.G12,E.G13
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG E.G15,E.G16
  strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG E.G22,E.G23
  strand#4 RNA glyco-bond=-- sugar=33 nts=2 GG E.G25,E.G26

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG E.G12,E.G15,E.G22,E.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG E.G13,E.G16,E.G23,E.G26
  step#1  pm(>>,forward)  area=10.56 rise=3.38 twist=32.5

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG Y.G12,Y.G15,Y.G22,Y.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG Y.G13,Y.G16,Y.G23,Y.G26
  step#1  pm(>>,forward)  area=10.84 rise=3.38 twist=33.3
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG Y.G12,Y.G13
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG Y.G15,Y.G16
  strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG Y.G22,Y.G23
  strand#4 RNA glyco-bond=-- sugar=33 nts=2 GG Y.G25,Y.G26

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG Y.G12,Y.G15,Y.G22,Y.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG Y.G13,Y.G16,Y.G23,Y.G26
  step#1  pm(>>,forward)  area=10.84 rise=3.38 twist=33.3

Download PDB file
Interactive view in 3Dmol.js

List of 2 G4-stems

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=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG E.G12,E.G15,E.G22,E.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG E.G13,E.G16,E.G23,E.G26
  step#1  pm(>>,forward)  area=10.56 rise=3.38 twist=32.5
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG E.G12,E.G13
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G15,E.G16
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG E.G22,E.G23
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G25,E.G26
  loop#1 type=propeller strands=[#1,#2] nts=1 A E.A14
  loop#2 type=propeller strands=[#2,#3] nts=5 uCUGA E.IU17,E.C18,E.U19,E.G20,E.A21
  loop#3 type=propeller strands=[#3,#4] nts=1 A E.A24

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG Y.G12,Y.G15,Y.G22,Y.G25
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG Y.G13,Y.G16,Y.G23,Y.G26
  step#1  pm(>>,forward)  area=10.84 rise=3.38 twist=33.3
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG Y.G12,Y.G13
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG Y.G15,Y.G16
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG Y.G22,Y.G23
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG Y.G25,Y.G26
  loop#1 type=propeller strands=[#1,#2] nts=1 A Y.A14
  loop#2 type=propeller strands=[#2,#3] nts=5 uCUGA Y.IU17,Y.C18,Y.U19,Y.G20,Y.A21
  loop#3 type=propeller strands=[#3,#4] nts=1 A Y.A24

Download PDB file
Interactive view in 3Dmol.js