Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
139d
Class
DNA
Method
NMR
Summary
Solution structure of a parallel-stranded G-quadruplex DNA
Reference
Wang, Y., Patel, D.J.: (1993) "Solution structure of a parallel-stranded G-quadruplex DNA." J.Mol.Biol., 234, 1171-1183.
Abstract
This paper reports on the solution structure of a parallel-stranded G-quadruplex formed by the Tetrahymena telomeric sequence d(T-T-G-G-G-G-T) whose NMR parameters in potassium cation containing solution were previously published from our laboratory. The structure was determined by combining a quantitative analysis of the NMR data with molecular dynamics calculations including relaxation matrix refinement. The combined NMR-computational approach yielded a set of seven distance-refined structures with pairwise RMSDs ranging from 0.66 to 1.30 A for the central G-G-G-G tetranucleotide segment. Four of the seven structures were refined further using complete relaxation-matrix calculations to yield solution structures with pairwise RMSDs ranging from 0.64 to 1.04 A for the same tetranucleotide segment. The R-factors also decreased on proceeding from the distance-refined to relaxation matrix-refined structures. The four strands of the G-quadruplex are aligned in parallel and are related by a 4-fold symmetry axis coincident with the helix axis. Individual guanines from each strand form planar G.G.G.G tetrad arrangements with each tetrad stabilized by eight hydrogen bonds involving the Watson-Crick and Hoogsteen edges of the guanine bases. All guanines adopt anti glycosidic torsion angles and S type sugar puckers in this right-handed parallel-stranded G-quadruplex structure. The four G.G.G.G tetrad planes stack on each other with minimal overlap of adjacent guanine base planes within individual strands. The thymine residues are under-defined in the solution structure of the d(T-T-G-G-G-G-T) G-quadruplex and sample amongst multiple conformations in solution.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.098 type=planar nts=4 GGGG A.DG3,D.DG3,C.DG3,B.DG3
 2 glyco-bond=---- groove=---- planarity=0.124 type=planar nts=4 GGGG A.DG4,D.DG4,C.DG4,B.DG4
 3 glyco-bond=---- groove=---- planarity=0.061 type=planar nts=4 GGGG A.DG5,D.DG5,C.DG5,B.DG5
 4 glyco-bond=---- groove=---- planarity=0.128 type=planar nts=4 GGGG A.DG6,D.DG6,C.DG6,B.DG6

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG3,C.DG3,B.DG3
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG4,C.DG4,B.DG4
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG5,C.DG5,B.DG5
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG6,C.DG6,B.DG6
  step#1  pm(>>,forward)  area=8.80  rise=3.02 twist=30.9
  step#2  pm(>>,forward)  area=6.76  rise=2.94 twist=37.0
  step#3  pm(>>,forward)  area=16.68 rise=3.15 twist=22.6
  strand#1 DNA glyco-bond=---- nts=4 GGGG A.DG3,A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=---- nts=4 GGGG D.DG3,D.DG4,D.DG5,D.DG6
  strand#3 DNA glyco-bond=---- nts=4 GGGG C.DG3,C.DG4,C.DG5,C.DG6
  strand#4 DNA glyco-bond=---- nts=4 GGGG B.DG3,B.DG4,B.DG5,B.DG6

Download PDB file
Interactive view in 3Dmol.js

3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG3,C.DG3,B.DG3
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG4,C.DG4,B.DG4
step#1 pm(>>,forward) area=8.80 rise=3.02 twist=30.9

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG4,C.DG4,B.DG4
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG5,C.DG5,B.DG5
step#2 pm(>>,forward) area=6.76 rise=2.94 twist=37.0

Download PDB file
Interactive view in 3Dmol.js

 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG5,C.DG5,B.DG5
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG6,C.DG6,B.DG6
step#3 pm(>>,forward) area=16.68 rise=3.15 twist=22.6

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG3,C.DG3,B.DG3
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG4,C.DG4,B.DG4
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG5,C.DG5,B.DG5
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG6,C.DG6,B.DG6
  step#1  pm(>>,forward)  area=8.80  rise=3.02 twist=30.9
  step#2  pm(>>,forward)  area=6.76  rise=2.94 twist=37.0
  step#3  pm(>>,forward)  area=16.68 rise=3.15 twist=22.6
  strand#1  U DNA glyco-bond=---- nts=4 GGGG A.DG3,A.DG4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=---- nts=4 GGGG D.DG3,D.DG4,D.DG5,D.DG6
  strand#3  U DNA glyco-bond=---- nts=4 GGGG C.DG3,C.DG4,C.DG5,C.DG6
  strand#4  U DNA glyco-bond=---- nts=4 GGGG B.DG3,B.DG4,B.DG5,B.DG6

Download PDB file
Interactive view in 3Dmol.js

List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)