DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 4rne
Class: RNA
Method: X-ray (1.01 Å)
Summary: Structural variations and solvent structure of uggggu quadruplexes stabilized by sr2+ ions
Reference: Fyfe AC, Dunten PW, Martick MM, Scott WG (2015): "Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr(2+) Ions." J.Mol.Biol., 427, 2205-2219. doi: 10.1016/j.jmb.2015.03.022.
Abstract: Guanine-rich sequences can, under appropriate conditions, adopt a distinctive, four-stranded, helical fold known as a G-quadruplex. Interest in quadruplex folds has grown in recent years as evidence of their biological relevance has accumulated from both sequence analysis and function-specific assays. The folds are unusually stable and their formation appears to require close management to maintain cell health; regulatory failure correlates with genomic instability and a number of cancer phenotypes. Biologically relevant quadruplex folds are anticipated to form transiently in mRNA and in single-stranded, unwound DNA. To elucidate factors, including bound solvent, that contribute to the stability of RNA quadruplexes, we examine, by X-ray crystallography and small-angle X-ray scattering, the structure of a previously reported tetramolecular quadruplex, UGGGGU stabilized by Sr(2+) ions. Crystal forms of the octameric assembly formed by this sequence exhibit unusually strong diffraction and anomalous signal enabling the construction of reliable models to a resolution of 0.88Å. The solvent structure confirms hydration patterns reported for other nucleic acid helical conformations and provides support for the greater stability of RNA quadruplexes relative to DNA. Novel features detected in the octameric RNA assembly include a new crystal form, evidence of multiple conformations and structural variations in the 3' U tetrad, including one that leads to the formation of a hydrated internal cavity.
G4 notes: 8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, parallel(4+0), UUUU, coaxial interfaces: 5'/5'

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

List of 8 G-tetrads

 1 glyco-bond=---- sugar=3333 groove=---- planarity=0.231 type=other  -- nts=4 GGGG 1:A.G102,1:B.G202,1:C.G302,1:D.G402
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.231 type=other  -- nts=4 GGGG 1:A.G103,1:B.G203,1:C.G303,1:D.G403
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.121 type=planar -- nts=4 GGGG 1:A.G104,1:B.G204,1:C.G304,1:D.G404
 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.283 type=bowl   -- nts=4 GGGG 1:A.G105,1:B.G205,1:C.G305,1:D.G405
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.231 type=other  -- nts=4 GGGG 2:A.G102,2:B.G202,2:C.G302,2:D.G402
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.231 type=other  -- nts=4 GGGG 2:A.G103,2:B.G203,2:C.G303,2:D.G403
 7 glyco-bond=---- sugar=3333 groove=---- planarity=0.121 type=planar -- nts=4 GGGG 2:A.G104,2:B.G204,2:C.G304,2:D.G404
 8 glyco-bond=---- sugar=3333 groove=---- planarity=0.283 type=bowl   -- nts=4 GGGG 2:A.G105,2:B.G205,2:C.G305,2:D.G405

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

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G105,1:B.G205,1:C.G305,1:D.G405 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G104,1:B.G204,1:C.G304,1:D.G404 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.G103,1:B.G203,1:C.G303,1:D.G403 4* glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G102,1:B.G202,1:C.G302,1:D.G402 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G302,2:B.G202,2:A.G102,2:D.G402 6 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 2:C.G303,2:B.G203,2:A.G103,2:D.G403 7 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G304,2:B.G204,2:A.G104,2:D.G404 8 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G305,2:B.G205,2:A.G105,2:D.G405 step#1 mp(<<,backward) area=13.47 rise=3.52 twist=24.3 step#2 mp(<<,backward) area=8.48 rise=3.17 twist=35.6 step#3 mp(<<,backward) area=11.68 rise=3.47 twist=27.7 step#4 mm(<>,outward) area=27.81 rise=3.19 twist=-31.0 step#5 pm(>>,forward) area=11.68 rise=3.47 twist=27.7 step#6 pm(>>,forward) area=8.48 rise=3.17 twist=35.6 step#7 pm(>>,forward) area=13.47 rise=3.52 twist=24.3 strand#1 RNA glyco-bond=-------- sugar=33-33-33 nts=8 GGGGGGGG 1:A.G105,1:A.G104,1:A.G103,1:A.G102,2:C.G302,2:C.G303,2:C.G304,2:C.G305 strand#2 RNA glyco-bond=-------- sugar=33-33-33 nts=8 GGGGGGGG 1:B.G205,1:B.G204,1:B.G203,1:B.G202,2:B.G202,2:B.G203,2:B.G204,2:B.G205 strand#3 RNA glyco-bond=-------- sugar=33-33-33 nts=8 GGGGGGGG 1:C.G305,1:C.G304,1:C.G303,1:C.G302,2:A.G102,2:A.G103,2:A.G104,2:A.G105 strand#4 RNA glyco-bond=-------- sugar=33-33-33 nts=8 GGGGGGGG 1:D.G405,1:D.G404,1:D.G403,1:D.G402,2:D.G402,2:D.G403,2:D.G404,2:D.G405 Download PDB file Interactive view in 3Dmol.js
7 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G105,1:B.G205,1:C.G305,1:D.G405 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G104,1:B.G204,1:C.G304,1:D.G404 step#1 mp(<<,backward) area=13.47 rise=3.52 twist=24.3 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G104,1:B.G204,1:C.G304,1:D.G404 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.G103,1:B.G203,1:C.G303,1:D.G403 step#2 mp(<<,backward) area=8.48 rise=3.17 twist=35.6 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.G103,1:B.G203,1:C.G303,1:D.G403 4* glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G102,1:B.G202,1:C.G302,1:D.G402 step#3 mp(<<,backward) area=11.68 rise=3.47 twist=27.7 Download PDB file Interactive view in 3Dmol.js
	4* glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G102,1:B.G202,1:C.G302,1:D.G402 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G302,2:B.G202,2:A.G102,2:D.G402 step#4 mm(<>,outward) area=27.81 rise=3.19 twist=-31.0 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G302,2:B.G202,2:A.G102,2:D.G402 6 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 2:C.G303,2:B.G203,2:A.G103,2:D.G403 step#5 pm(>>,forward) area=11.68 rise=3.47 twist=27.7 Download PDB file Interactive view in 3Dmol.js
	6 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 2:C.G303,2:B.G203,2:A.G103,2:D.G403 7 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G304,2:B.G204,2:A.G104,2:D.G404 step#6 pm(>>,forward) area=8.48 rise=3.17 twist=35.6 Download PDB file Interactive view in 3Dmol.js
	7 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G304,2:B.G204,2:A.G104,2:D.G404 8 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 2:C.G305,2:B.G205,2:A.G105,2:D.G405 step#7 pm(>>,forward) area=13.47 rise=3.52 twist=24.3 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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G102,1:B.G202,1:C.G302,1:D.G402
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.G103,1:B.G203,1:C.G303,1:D.G403
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G104,1:B.G204,1:C.G304,1:D.G404
 4  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.G105,1:B.G205,1:C.G305,1:D.G405
  step#1  pm(>>,forward)  area=11.68 rise=3.47 twist=27.7
  step#2  pm(>>,forward)  area=8.48  rise=3.17 twist=35.6
  step#3  pm(>>,forward)  area=13.47 rise=3.52 twist=24.3
  strand#1  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 1:A.G102,1:A.G103,1:A.G104,1:A.G105
  strand#2  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 1:B.G202,1:B.G203,1:B.G204,1:B.G205
  strand#3  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 1:C.G302,1:C.G303,1:C.G304,1:C.G305
  strand#4  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 1:D.G402,1:D.G403,1:D.G404,1:D.G405

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Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 2:A.G102,2:B.G202,2:C.G302,2:D.G402
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.G103,2:B.G203,2:C.G303,2:D.G403
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 2:A.G104,2:B.G204,2:C.G304,2:D.G404
 4  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 2:A.G105,2:B.G205,2:C.G305,2:D.G405
  step#1  pm(>>,forward)  area=11.68 rise=3.47 twist=27.7
  step#2  pm(>>,forward)  area=8.48  rise=3.17 twist=35.6
  step#3  pm(>>,forward)  area=13.47 rise=3.52 twist=24.3
  strand#1  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 2:A.G102,2:A.G103,2:A.G104,2:A.G105
  strand#2  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 2:B.G202,2:B.G203,2:B.G204,2:B.G205
  strand#3  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 2:C.G302,2:C.G303,2:C.G304,2:C.G305
  strand#4  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 2:D.G402,2:D.G403,2:D.G404,2:D.G405