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

PDB-id
1k8p
Class
DNA
Method
X-ray (2.4 Å)
Summary
Structure of the human G-quadruplex reveals a novel topology
Reference
Parkinson, G.N., Lee, M.P., Neidle, S.: (2002) "Crystal structure of parallel quadruplexes from human telomeric DNA." Nature, 417, 876-880.
Abstract
Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, are fundamental in protecting the cell from recombination and degradation. Disruption of telomere maintenance leads to eventual cell death, which can be exploited for therapeutic intervention in cancer. Telomeric DNA sequences can form four-stranded (quadruplex) structures, which may be involved in the structure of telomere ends. Here we describe the crystal structure of a quadruplex formed from four consecutive human telomeric DNA repeats and grown at a K(+) concentration that approximates its intracellular concentration. K(+) ions are observed in the structure. The folding and appearance of the DNA in this intramolecular quadruplex is fundamentally different from the published Na(+)-containing quadruplex structures. All four DNA strands are parallel, with the three linking trinucleotide loops positioned on the exterior of the quadruplex core, in a propeller-like arrangement. The adenine in each TTA linking trinucleotide loop is swung back so that it intercalates between the two thymines. This DNA structure suggests a straightforward path for telomere folding and unfolding, as well as ways in which it can recognize telomere-associated proteins.
G4 notes
3 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 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.201 type=other  nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2 glyco-bond=---- groove=---- planarity=0.170 type=other  nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3 glyco-bond=---- groove=---- planarity=0.331 type=bowl   nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23

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, 3 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
  step#1  pm(>>,forward)  area=9.08  rise=3.37 twist=32.4
  step#2  pm(>>,forward)  area=11.15 rise=3.42 twist=27.1
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG21,B.DG22,B.DG23

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
step#1 pm(>>,forward) area=9.08 rise=3.37 twist=32.4

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
step#2 pm(>>,forward) area=11.15 rise=3.42 twist=27.1

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
  step#1  pm(>>,forward)  area=9.08  rise=3.37 twist=32.4
  step#2  pm(>>,forward)  area=11.15 rise=3.42 twist=27.1
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG21,B.DG22,B.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 uTA A.BRU6,A.DT7,A.DA8
  loop#2 type=propeller strands=[#3,#4] nts=3 uTA B.BRU18,B.DT19,B.DA20

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

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