Summary information and primary citation

PDB-id
4ts0
Class
RNA
Method
X-ray (2.8 Å)
Summary
Crystal structure of the spinach RNA aptamer in complex with dfhbi, barium ions
Reference
Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, Ferre-D'Amare AR (2014): "Structural basis for activity of highly efficient RNA mimics of green fluorescent protein." Nat.Struct.Mol.Biol., 21, 658-663. doi: 10.1038/nsmb.2865.
Abstract
GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to large RNA-binding protein-GFP fusions. To elucidate the molecular basis of Spinach fluorescence, we solved the cocrystal structure of Spinach bound to its cognate exogenous chromophore, showing that Spinach activates the small molecule by immobilizing it between a base triple, a G-quadruplex and an unpaired G. Mutational and NMR analyses indicate that the G-quadruplex is essential for Spinach fluorescence, is also present in other fluorogenic RNAs and may represent a general strategy for RNAs to induce fluorescence of chromophores. The structure guided the design of a miniaturized 'Baby Spinach', and it provides a foundation for structure-driven design and tuning of fluorescent RNAs.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, UUDD, anti-parallel:basket2, 2+2

Cartoon-block schematics in six views (download the tarball)

PyMOL session file

Download 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 X.G25,X.G29,Y.G72,Y.G68
 2 glyco-bond=--ss sugar=-3-3 groove=-w-n planarity=0.172 type=other  -- nts=4 GGGG X.G26,X.G30,Y.G70,Y.G65

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-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=--s- sugar=-33. groove=-wn- WC-->Major -- nts=4 GGGG X.G25,X.G29,Y.G72,Y.G68
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major -- nts=4 GGGG X.G26,X.G30,Y.G70,Y.G65
  step#1  pm(>>,forward)  area=9.81  rise=3.30 twist=32.8
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG X.G25,X.G26
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG X.G29,X.G30
  strand#3 RNA glyco-bond=ss sugar=3- nts=2 GG Y.G72,Y.G70
  strand#4 RNA glyco-bond=-s sugar=.3 nts=2 GG Y.G68,Y.G65

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=--s- sugar=-33. groove=-wn- WC-->Major -- nts=4 GGGG X.G25,X.G29,Y.G72,Y.G68
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major -- nts=4 GGGG X.G26,X.G30,Y.G70,Y.G65
  step#1  pm(>>,forward)  area=9.81  rise=3.30 twist=32.8

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-tetrads, 2 loops, inter-molecular, UUDD, anti-parallel:basket2, 2+2
 1  glyco-bond=--s- sugar=-33. groove=-wn- WC-->Major -- nts=4 GGGG X.G25,X.G29,Y.G72,Y.G68
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major -- nts=4 GGGG X.G26,X.G30,Y.G70,Y.G65
  step#1  pm(>>,forward)  area=9.81  rise=3.30 twist=32.8
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG X.G25,X.G26
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG X.G29,X.G30
  strand#3* D RNA glyco-bond=ss sugar=3- nts=2 GG Y.G72,Y.G70 bulged-nts=1 U Y.U71
  strand#4* D RNA glyco-bond=-s sugar=.3 nts=2 GG Y.G68,Y.G65 bulged-nts=2 AU Y.A67,Y.U66
  loop#1 type=propeller strands=[#1,#2] nts=2 AC X.A27,X.C28
  loop#2 type=propeller strands=[#4,#3] nts=1 A Y.A69

Download PDB file
Interactive view in 3Dmol.js