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

PDB-id
3tvb*
Class
DNA-antibiotic
Method
X-ray (1.08 Å)
Summary
A highly symmetric DNA g-4 quadruplex-drug complex
Reference
Clark, G.R., Pytel, P.D., Squire, C.J.: (2012) "The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages." Nucleic Acids Res., 40, 5731-5738.
Abstract
We have determined the X-ray structure of the complex between the DNA quadruplex d(5'-GGGG-3')(4) and daunomycin, as a potential model for studying drug-telomere interactions. The structure was solved at 1.08 Å by direct methods in space group I4. The asymmetric unit comprises a linear arrangement of one d(GGGG) strand, four daunomycin molecules, a second d(GGGG) strand facing in the opposite direction to the first, and Na and Mg cations. The crystallographic 4-fold axis generates the biological unit, which is a 12-layered structure comprising two sets of four guanine layers, with four layers each of four daunomycins stacked between the 5' faces of the two quadruplexes. The daunomycin layers fall into two groups which are novel in their mode of self assembly. The only contacts between daunomycin molecules within any one of these layers are van der Waals interactions, however there is substantial π-π stacking between successive daunomycin layers and also with adjacent guanine layers. The structure differs significantly from all other parallel d(TGGGGT)(4) quadruplexes in that the 5' guanine adopts the unusual syn glycosyl linkage, refuting the widespread belief that such conformations should all be anti. In contrast to the related d(TGGGGT)/daunomycin complex, there are no ligand-quadruplex groove insertion interactions.
G4 notes
8 G-tetrads, 2 G4 helices, 2 G4 stems · parallel(4+0), UUUU

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

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List of 8 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=ssss groove=---- planarity=0.075 type=planar nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1
 2 glyco-bond=---- groove=---- planarity=0.198 type=other  nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2
 3 glyco-bond=---- groove=---- planarity=0.108 type=planar nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3
 4 glyco-bond=---- groove=---- planarity=0.312 type=bowl   nts=4 GGGG 1:A.DG4,4:A.DG4,2:A.DG4,3:A.DG4
 5 glyco-bond=ssss groove=---- planarity=0.060 type=planar nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5
 6 glyco-bond=---- groove=---- planarity=0.163 type=other  nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6
 7 glyco-bond=---- groove=---- planarity=0.098 type=planar nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
 8 glyco-bond=---- groove=---- planarity=0.311 type=bowl   nts=4 GGGG 1:B.DG8,3:B.DG8,2:B.DG8,4:B.DG8

List of 2 G4-helices [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=ssss groove=---- Major-->WC nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG4,4:A.DG4,2:A.DG4,3:A.DG4
  step#1  mm(<>,outward)  area=12.41 rise=3.45 twist=20.5
  step#2  pm(>>,forward)  area=9.06  rise=3.21 twist=33.7
  step#3  pm(>>,forward)  area=14.52 rise=3.45 twist=22.2
  strand#1 DNA glyco-bond=s--- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2 DNA glyco-bond=s--- nts=4 GGGG 4:A.DG1,4:A.DG2,4:A.DG3,4:A.DG4
  strand#3 DNA glyco-bond=s--- nts=4 GGGG 2:A.DG1,2:A.DG2,2:A.DG3,2:A.DG4
  strand#4 DNA glyco-bond=s--- nts=4 GGGG 3:A.DG1,3:A.DG2,3:A.DG3,3:A.DG4

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3 stacking diagrams
 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2
step#1 mm(<>,outward) area=12.41 rise=3.45 twist=20.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3
step#2 pm(>>,forward) area=9.06 rise=3.21 twist=33.7

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG4,4:A.DG4,2:A.DG4,3:A.DG4
step#3 pm(>>,forward) area=14.52 rise=3.45 twist=22.2

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Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG8,3:B.DG8,2:B.DG8,4:B.DG8
  step#1  mm(<>,outward)  area=11.40 rise=3.46 twist=22.1
  step#2  pm(>>,forward)  area=9.24  rise=3.22 twist=33.3
  step#3  pm(>>,forward)  area=14.60 rise=3.47 twist=22.8
  strand#1 DNA glyco-bond=s--- nts=4 GGGG 1:B.DG5,1:B.DG6,1:B.DG7,1:B.DG8
  strand#2 DNA glyco-bond=s--- nts=4 GGGG 3:B.DG5,3:B.DG6,3:B.DG7,3:B.DG8
  strand#3 DNA glyco-bond=s--- nts=4 GGGG 2:B.DG5,2:B.DG6,2:B.DG7,2:B.DG8
  strand#4 DNA glyco-bond=s--- nts=4 GGGG 4:B.DG5,4:B.DG6,4:B.DG7,4:B.DG8

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3 stacking diagrams
 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6
step#1 mm(<>,outward) area=11.40 rise=3.46 twist=22.1

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
step#2 pm(>>,forward) area=9.24 rise=3.22 twist=33.3

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG8,3:B.DG8,2:B.DG8,4:B.DG8
step#3 pm(>>,forward) area=14.60 rise=3.47 twist=22.8

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List of 2 G4-stems [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=ssss groove=---- Major-->WC nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG4,4:A.DG4,2:A.DG4,3:A.DG4
  step#1  mm(<>,outward)  area=12.41 rise=3.45 twist=20.5
  step#2  pm(>>,forward)  area=9.06  rise=3.21 twist=33.7
  step#3  pm(>>,forward)  area=14.52 rise=3.45 twist=22.2
  strand#1  U DNA glyco-bond=s--- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2  U DNA glyco-bond=s--- nts=4 GGGG 4:A.DG1,4:A.DG2,4:A.DG3,4:A.DG4
  strand#3  U DNA glyco-bond=s--- nts=4 GGGG 2:A.DG1,2:A.DG2,2:A.DG3,2:A.DG4
  strand#4  U DNA glyco-bond=s--- nts=4 GGGG 3:A.DG1,3:A.DG2,3:A.DG3,3:A.DG4

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

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG8,3:B.DG8,2:B.DG8,4:B.DG8
  step#1  mm(<>,outward)  area=11.40 rise=3.46 twist=22.1
  step#2  pm(>>,forward)  area=9.24  rise=3.22 twist=33.3
  step#3  pm(>>,forward)  area=14.60 rise=3.47 twist=22.8
  strand#1  U DNA glyco-bond=s--- nts=4 GGGG 1:B.DG5,1:B.DG6,1:B.DG7,1:B.DG8
  strand#2  U DNA glyco-bond=s--- nts=4 GGGG 3:B.DG5,3:B.DG6,3:B.DG7,3:B.DG8
  strand#3  U DNA glyco-bond=s--- nts=4 GGGG 2:B.DG5,2:B.DG6,2:B.DG7,2:B.DG8
  strand#4  U DNA glyco-bond=s--- nts=4 GGGG 4:B.DG5,4:B.DG6,4:B.DG7,4:B.DG8

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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)