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

PDB-id
1s45
Class
DNA
Method
X-ray (2.2 Å)
Summary
Crystal structure analysis of the DNA quadruplex d(tggggt) s1
Reference
Caceres, C., Wright, G., Gouyette, C., Parkinson, G., Subirana, J.A.: (2004) "A Thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+1/Na+1 ions." Nucleic Acids Res., 32, 1097-1102.
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
8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

PyMOL session file PDB file View in 3Dmol.js

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

 1 glyco-bond=---- groove=---- planarity=0.098 type=planar nts=4 GGGG A.DG182,D.DG512,C.DG402,B.DG292
 2 glyco-bond=---- groove=---- planarity=0.218 type=bowl   nts=4 GGGG A.DG183,D.DG513,C.DG403,B.DG293
 3 glyco-bond=---- groove=---- planarity=0.191 type=other  nts=4 GGGG A.DG184,D.DG514,C.DG404,B.DG294
 4 glyco-bond=---- groove=---- planarity=0.247 type=bowl   nts=4 GGGG A.DG185,D.DG515,C.DG405,B.DG295
 5 glyco-bond=---- groove=---- planarity=0.332 type=bowl   nts=4 GGGG E.DG622,H.DG952,G.DG842,F.DG732
 6 glyco-bond=---- groove=---- planarity=0.191 type=other  nts=4 GGGG E.DG623,H.DG953,G.DG843,F.DG733
 7 glyco-bond=---- groove=---- planarity=0.094 type=planar nts=4 GGGG E.DG624,H.DG954,G.DG844,F.DG734
 8 glyco-bond=---- groove=---- planarity=0.214 type=bowl   nts=4 GGGG E.DG625,H.DG955,G.DG845,F.DG735

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, 8 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG185,D.DG515,C.DG405,B.DG295
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG184,D.DG514,C.DG404,B.DG294
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG183,D.DG513,C.DG403,B.DG293
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG182,D.DG512,C.DG402,B.DG292
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG622,F.DG732,G.DG842,H.DG952
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG623,F.DG733,G.DG843,H.DG953
 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG624,F.DG734,G.DG844,H.DG954
 8  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG625,F.DG735,G.DG845,H.DG955
  step#1  mp(<<,backward) area=13.37 rise=3.37 twist=25.8
  step#2  mp(<<,backward) area=9.27  rise=3.40 twist=31.8
  step#3  mp(<<,backward) area=9.60  rise=3.57 twist=28.9
  step#4  mm(<>,outward)  area=11.20 rise=3.79 twist=18.1
  step#5  pm(>>,forward)  area=11.49 rise=3.35 twist=30.1
  step#6  pm(>>,forward)  area=10.01 rise=3.26 twist=30.0
  step#7  pm(>>,forward)  area=13.12 rise=3.37 twist=27.1
  strand#1 DNA glyco-bond=-------- nts=8 GGGGGGGG A.DG185,A.DG184,A.DG183,A.DG182,E.DG622,E.DG623,E.DG624,E.DG625
  strand#2 DNA glyco-bond=-------- nts=8 GGGGGGGG D.DG515,D.DG514,D.DG513,D.DG512,F.DG732,F.DG733,F.DG734,F.DG735
  strand#3 DNA glyco-bond=-------- nts=8 GGGGGGGG C.DG405,C.DG404,C.DG403,C.DG402,G.DG842,G.DG843,G.DG844,G.DG845
  strand#4 DNA glyco-bond=-------- nts=8 GGGGGGGG B.DG295,B.DG294,B.DG293,B.DG292,H.DG952,H.DG953,H.DG954,H.DG955

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG185,D.DG515,C.DG405,B.DG295
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG184,D.DG514,C.DG404,B.DG294
step#1 mp(<<,backward) area=13.37 rise=3.37 twist=25.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG184,D.DG514,C.DG404,B.DG294
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG183,D.DG513,C.DG403,B.DG293
step#2 mp(<<,backward) area=9.27 rise=3.40 twist=31.8

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG183,D.DG513,C.DG403,B.DG293
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG182,D.DG512,C.DG402,B.DG292
step#3 mp(<<,backward) area=9.60 rise=3.57 twist=28.9

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG182,D.DG512,C.DG402,B.DG292
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG622,F.DG732,G.DG842,H.DG952
step#4 mm(<>,outward) area=11.20 rise=3.79 twist=18.1

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG622,F.DG732,G.DG842,H.DG952
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG623,F.DG733,G.DG843,H.DG953
step#5 pm(>>,forward) area=11.49 rise=3.35 twist=30.1

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 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG623,F.DG733,G.DG843,H.DG953
7 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG624,F.DG734,G.DG844,H.DG954
step#6 pm(>>,forward) area=10.01 rise=3.26 twist=30.0

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 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG624,F.DG734,G.DG844,H.DG954
8 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG625,F.DG735,G.DG845,H.DG955
step#7 pm(>>,forward) area=13.12 rise=3.37 twist=27.1

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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=---- groove=---- WC-->Major nts=4 GGGG A.DG182,D.DG512,C.DG402,B.DG292
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG183,D.DG513,C.DG403,B.DG293
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG184,D.DG514,C.DG404,B.DG294
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG185,D.DG515,C.DG405,B.DG295
  step#1  pm(>>,forward)  area=9.60  rise=3.57 twist=28.9
  step#2  pm(>>,forward)  area=9.27  rise=3.40 twist=31.8
  step#3  pm(>>,forward)  area=13.37 rise=3.37 twist=25.8
  strand#1  U DNA glyco-bond=---- nts=4 GGGG A.DG182,A.DG183,A.DG184,A.DG185
  strand#2  U DNA glyco-bond=---- nts=4 GGGG D.DG512,D.DG513,D.DG514,D.DG515
  strand#3  U DNA glyco-bond=---- nts=4 GGGG C.DG402,C.DG403,C.DG404,C.DG405
  strand#4  U DNA glyco-bond=---- nts=4 GGGG B.DG292,B.DG293,B.DG294,B.DG295

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG622,H.DG952,G.DG842,F.DG732
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG623,H.DG953,G.DG843,F.DG733
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG624,H.DG954,G.DG844,F.DG734
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG625,H.DG955,G.DG845,F.DG735
  step#1  pm(>>,forward)  area=11.49 rise=3.35 twist=30.1
  step#2  pm(>>,forward)  area=10.01 rise=3.26 twist=30.0
  step#3  pm(>>,forward)  area=13.12 rise=3.37 twist=27.1
  strand#1  U DNA glyco-bond=---- nts=4 GGGG E.DG622,E.DG623,E.DG624,E.DG625
  strand#2  U DNA glyco-bond=---- nts=4 GGGG H.DG952,H.DG953,H.DG954,H.DG955
  strand#3  U DNA glyco-bond=---- nts=4 GGGG G.DG842,G.DG843,G.DG844,G.DG845
  strand#4  U DNA glyco-bond=---- nts=4 GGGG F.DG732,F.DG733,F.DG734,F.DG735

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

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