Summary information and primary citation

PDB-id
1k8p
Class
DNA
Method
X-ray (2.4 Å)
Summary
Structure of the human g-quadruplex reveals a novel topology
Reference
Parkinson GN, Lee MP, Neidle S (2002): "Crystal structure of parallel quadruplexes from human telomeric DNA." Nature, 417, 876-880. doi: 10.1038/nature755.
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, UUUU, parallel, 4+0

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

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List of 3 G-tetrads

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

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, 3 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=---- sugar=---. groove=---- WC-->Major -- nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major -- nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- sugar=---- 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=--- sugar=-3- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4 DNA glyco-bond=--- sugar=.-- nts=3 GGG B.DG21,B.DG22,B.DG23

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---. groove=---- WC-->Major -- nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- sugar=3--- 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=---- sugar=3--- groove=---- WC-->Major -- nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- sugar=---- 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

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-tetrads, 2 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=---. groove=---- WC-->Major -- nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major -- nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- sugar=---- 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=--- sugar=-3- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4  U DNA glyco-bond=--- sugar=.-- 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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