Summary information and primary citation

PDB-id
1s47
Class
DNA
Method
X-ray (2.5 Å)
Summary
Crystal structure analysis of the DNA quadruplex d(tggggt)s2
Reference
Caceres C, Wright G, Gouyette C, Parkinson G, Subirana JA (2004): "A Thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+1/Na+1 ions." Nucleic Acids Res., 32, 1097-1102. doi: 10.1093/nar/gkh269.
Abstract
We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG1-3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3'ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na+ or Tl+ ions. We show that by using MAD methods, Tl+ can be unambiguously located and distinguished from Na+. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0

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

PyMOL session file

Download PDB file

View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.152 type=planar -- nts=4 GGGG 1:A.DG102,1:D.DG432,1:C.DG322,1:B.DG212
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.186 type=bowl-2 -- nts=4 GGGG 1:A.DG103,1:D.DG433,1:C.DG323,1:B.DG213
 3 glyco-bond=---- sugar=.--- groove=---- planarity=0.173 type=other  -- nts=4 GGGG 1:A.DG104,1:D.DG434,1:C.DG324,1:B.DG214
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.280 type=bowl   -- nts=4 GGGG 1:A.DG105,1:D.DG435,1:C.DG325,1:B.DG215

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 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG102,1:D.DG432,1:C.DG322,1:B.DG212
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG103,1:D.DG433,1:C.DG323,1:B.DG213
 3  glyco-bond=---- sugar=.--- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG104,1:D.DG434,1:C.DG324,1:B.DG214
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG105,1:D.DG435,1:C.DG325,1:B.DG215
  step#1  pm(>>,forward)  area=16.35 rise=3.25 twist=24.5
  step#2  pm(>>,forward)  area=9.58  rise=3.30 twist=33.1
  step#3  pm(>>,forward)  area=10.61 rise=3.37 twist=27.0
  strand#1 DNA glyco-bond=---- sugar=--.- nts=4 GGGG 1:A.DG102,1:A.DG103,1:A.DG104,1:A.DG105
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:D.DG432,1:D.DG433,1:D.DG434,1:D.DG435
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:C.DG322,1:C.DG323,1:C.DG324,1:C.DG325
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:B.DG212,1:B.DG213,1:B.DG214,1:B.DG215

Download PDB file
Interactive view in 3Dmol.js
3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG102,1:D.DG432,1:C.DG322,1:B.DG212
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG103,1:D.DG433,1:C.DG323,1:B.DG213
  step#1  pm(>>,forward)  area=16.35 rise=3.25 twist=24.5

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG103,1:D.DG433,1:C.DG323,1:B.DG213
 3  glyco-bond=---- sugar=.--- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG104,1:D.DG434,1:C.DG324,1:B.DG214
  step#2  pm(>>,forward)  area=9.58  rise=3.30 twist=33.1

Download PDB file
Interactive view in 3Dmol.js

 
 3  glyco-bond=---- sugar=.--- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG104,1:D.DG434,1:C.DG324,1:B.DG214
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG105,1:D.DG435,1:C.DG325,1:B.DG215
  step#3  pm(>>,forward)  area=10.61 rise=3.37 twist=27.0

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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG102,1:D.DG432,1:C.DG322,1:B.DG212
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG103,1:D.DG433,1:C.DG323,1:B.DG213
 3  glyco-bond=---- sugar=.--- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG104,1:D.DG434,1:C.DG324,1:B.DG214
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG105,1:D.DG435,1:C.DG325,1:B.DG215
  step#1  pm(>>,forward)  area=16.35 rise=3.25 twist=24.5
  step#2  pm(>>,forward)  area=9.58  rise=3.30 twist=33.1
  step#3  pm(>>,forward)  area=10.61 rise=3.37 twist=27.0
  strand#1  U DNA glyco-bond=---- sugar=--.- nts=4 GGGG 1:A.DG102,1:A.DG103,1:A.DG104,1:A.DG105
  strand#2  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:D.DG432,1:D.DG433,1:D.DG434,1:D.DG435
  strand#3  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:C.DG322,1:C.DG323,1:C.DG324,1:C.DG325
  strand#4  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:B.DG212,1:B.DG213,1:B.DG214,1:B.DG215

Download PDB file
Interactive view in 3Dmol.js