DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 6ge1
Class: RNA
Method: NMR
Summary: Solution structure of the r(ugguggu)4 RNA quadruplex
Reference: Andralojc W, Malgowska M, Sarzynska J, Pasternak K, Szpotkowski K, Kierzek R, Gdaniec Z (2019): "Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus." RNA, 25, 121-134. doi: 10.1261/rna.068163.118.
Abstract: Uridine tetrads (U-tetrads) are a structural element encountered in RNA G-quadruplexes, for example, in the structures formed by the biologically relevant human telomeric repeat RNA. For these molecules, an unexpectedly strong stabilizing influence of a U-tetrad forming at the 3' terminus of a quadruplex was reported. Here we present the high-resolution solution NMR structure of the r(UGGUGGU)<sub>4</sub> quadruplex which, in our opinion, provides an explanation for this stabilization. Our structure features a distinctive, abrupt chain reversal just prior to the 3' uridine tetrad. Similar "reversed U-tetrads" were already observed in the crystalline phase. However, our NMR structure coupled with extensive explicit solvent molecular dynamics (MD) simulations identifies some key features of this motif that up to now remained overlooked. These include the presence of an exceptionally stable 2'OH to phosphate hydrogen bond, as well as the formation of an additional K<sub>+</sub> binding pocket in the quadruplex groove.
G4 notes: 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, coaxial interfaces: 3'/5'

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

List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.167 type=other  -- nts=4 GGGG A.G2,D.G2,C.G2,B.G2
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.262 type=other  -- nts=4 GGGG A.G3,D.G3,C.G3,B.G3
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.111 type=planar -- nts=4 GGGG A.G5,D.G5,C.G5,B.G5
 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.368 type=bowl   -- nts=4 GGGG A.G6,D.G6,C.G6,B.G6

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, 4 G-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G2,D.G2,C.G2,B.G2 2* glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G3,D.G3,C.G3,B.G3 3 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG A.G5,B.G5,C.G5,D.G5 4 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG A.G6,B.G6,C.G6,D.G6 step#1 pm(>>,forward) area=10.68 rise=3.18 twist=34.6 step#2 pm(>>,forward) area=0.00 rise=7.06 twist=152.6 step#3 pm(>>,forward) area=17.62 rise=3.66 twist=19.8 strand#1 RNA glyco-bond=---- sugar=-333 nts=4 GGGG A.G2,A.G3,A.G5,A.G6 strand#2 RNA glyco-bond=---- sugar=-333 nts=4 GGGG D.G2,D.G3,B.G5,B.G6 strand#3 RNA glyco-bond=---- sugar=-333 nts=4 GGGG C.G2,C.G3,C.G5,C.G6 strand#4 RNA glyco-bond=---- sugar=-333 nts=4 GGGG B.G2,B.G3,D.G5,D.G6 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G2,D.G2,C.G2,B.G2 2* glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G3,D.G3,C.G3,B.G3 step#1 pm(>>,forward) area=10.68 rise=3.18 twist=34.6 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G3,D.G3,C.G3,B.G3 3 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG A.G5,B.G5,C.G5,D.G5 step#2 pm(>>,forward) area=0.00 rise=7.06 twist=152.6 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG A.G5,B.G5,C.G5,D.G5 4 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG A.G6,B.G6,C.G6,D.G6 step#3 pm(>>,forward) area=17.62 rise=3.66 twist=19.8 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-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G2,D.G2,C.G2,B.G2
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G3,D.G3,C.G3,B.G3
  step#1  pm(>>,forward)  area=10.68 rise=3.18 twist=34.6
  strand#1  U RNA glyco-bond=-- sugar=-3 nts=2 GG A.G2,A.G3
  strand#2  U RNA glyco-bond=-- sugar=-3 nts=2 GG D.G2,D.G3
  strand#3  U RNA glyco-bond=-- sugar=-3 nts=2 GG C.G2,C.G3
  strand#4  U RNA glyco-bond=-- sugar=-3 nts=2 GG B.G2,B.G3

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 2 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G5,D.G5,C.G5,B.G5
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G6,D.G6,C.G6,B.G6
  step#1  pm(>>,forward)  area=17.62 rise=3.66 twist=19.8
  strand#1  U RNA glyco-bond=-- sugar=33 nts=2 GG A.G5,A.G6
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG D.G5,D.G6
  strand#3  U RNA glyco-bond=-- sugar=33 nts=2 GG C.G5,C.G6
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG B.G5,B.G6