DSSR-curated G4 structure: PDB entry 2led

Summary information

PDB id: 2led
Class: DNA
Method: NMR
Summary: Unique structural features of interconverting monomeric and dimeric g-quadruplexes adopted by a sequence from intron of n-myc gene
Reference: Trajkovski M, Webba da Silva M, Plavec J (2012): "Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene." J.Am.Chem.Soc., 134, 4132-4141. doi: 10.1021/ja208483v.
Abstract: A multidimensional heteronuclear NMR study has demonstrated that a guanine-rich DNA oligonucleotide originating from the N-myc gene folds into G-quadruplex structures in the presence of K(+), NH(4)(+), and Na(+) ions. A monomeric G-quadruplex formed in K(+) ion containing solution exhibits three G-quartets and flexible propeller-type loops. The 3D structure with three single nucleotide loops represents a missing element in structures of parallel G-quadruplexes. The structural features together with the high temperature stability are suggestive of the specific biological role of G-quadruplex formation within the intron of the N-myc gene. An increase in K(+) ion and oligonucleotide concentrations resulted in transformation of the monomeric G-quadruplex into a dimeric form. The dimeric G-quadruplex exhibits six stacked G-quartets, parallel strand orientations, and propeller-type loops. A link between the third and the fourth G-quartets consists of two adenine residues that are flipped out to facilitate consecutive stacking of six G-quartets.
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, parallel(4+0), UUUU, coaxial interfaces: 3'/5'

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.399 type=other  nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.447 type=bowl   nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.313 type=other  nts=4 GGGG A.DG5,A.DG9,B.DG5,B.DG9
 4 glyco-bond=---- sugar=-.-- groove=---- planarity=0.188 type=other  nts=4 GGGG A.DG11,A.DG15,B.DG11,B.DG15
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.229 type=bowl   nts=4 GGGG A.DG12,A.DG16,B.DG12,B.DG16
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.447 type=bowl   nts=4 GGGG A.DG13,A.DG17,B.DG13,B.DG17

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, 6 G-tetrad layers, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,B.DG5,B.DG9 4 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG B.DG15,A.DG11,A.DG15,B.DG11 5 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG16,A.DG12,A.DG16,B.DG12 6 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG17,A.DG13,A.DG17,B.DG13 step#1 pm(>>,forward) area=17.43 rise=3.67 twist=14.2 step#2 pm(>>,forward) area=7.63 rise=3.49 twist=29.5 step#3 pm(>>,forward) area=10.89 rise=3.14 twist=31.9 step#4 pm(>>,forward) area=12.19 rise=3.53 twist=26.4 step#5 pm(>>,forward) area=12.11 rise=3.54 twist=25.0 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG3,A.DG4,A.DG5,B.DG15,B.DG16,B.DG17 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG7,A.DG8,A.DG9,A.DG11,A.DG12,A.DG13 strand#3 DNA glyco-bond=------ sugar=---.-- nts=6 GGGGGG B.DG3,B.DG4,B.DG5,A.DG15,A.DG16,A.DG17 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG B.DG7,B.DG8,B.DG9,B.DG11,B.DG12,B.DG13 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8 step#1 pm(>>,forward) area=17.43 rise=3.67 twist=14.2 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,B.DG5,B.DG9 step#2 pm(>>,forward) area=7.63 rise=3.49 twist=29.5 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,B.DG5,B.DG9 4 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG B.DG15,A.DG11,A.DG15,B.DG11 step#3 pm(>>,forward) area=10.89 rise=3.14 twist=31.9 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG B.DG15,A.DG11,A.DG15,B.DG11 5 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG16,A.DG12,A.DG16,B.DG12 step#4 pm(>>,forward) area=12.19 rise=3.53 twist=26.4 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG16,A.DG12,A.DG16,B.DG12 6 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG17,A.DG13,A.DG17,B.DG13 step#5 pm(>>,forward) area=12.11 rise=3.54 twist=25.0 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, 3 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,B.DG5,B.DG9
  step#1  pm(>>,forward)  area=17.43 rise=3.67 twist=14.2
  step#2  pm(>>,forward)  area=7.63  rise=3.49 twist=29.5
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC6
  loop#2 type=propeller strands=[#3,#4] nts=1 C B.DC6

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

 1  glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG11,A.DG15,B.DG11,B.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG12,A.DG16,B.DG12,B.DG16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG13,A.DG17,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=12.19 rise=3.53 twist=26.4
  step#2  pm(>>,forward)  area=12.11 rise=3.54 twist=25.0
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#2  U DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG15,A.DG16,A.DG17
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA14
  loop#2 type=propeller strands=[#3,#4] nts=1 A B.DA14