Summary information and primary citation

PDB-id
7ll0
Class
DNA
Method
X-ray (2.0 Å)
Summary
Crystal structure of a four-tetrad, parallel, and k+ stabilized tetrahymena thermophila telomeric g-quadruplex
Reference
Beseiso D, Chen EV, McCarthy SE, Martin KN, Gallagher EP, Miao J, Yatsunyk LA (2022): "The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes." Nucleic Acids Res., 50, 2959-2972. doi: 10.1093/nar/gkac091.
Abstract
G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3'-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5'-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 4(-P-P-P)

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

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List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.048 type=planar O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.095 type=planar O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3 glyco-bond=---- sugar=--.- groove=---- planarity=0.145 type=planar O+ nts=4 GGGG A.DG6,A.DG12,A.DG18,A.DG24
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.275 type=bowl   O+ nts=4 GGGG A.DG7,A.DG13,A.DG19,A.DG25

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, 4 G-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3  glyco-bond=---- sugar=--.- groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG12,A.DG18,A.DG24
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG7,A.DG13,A.DG19,A.DG25
  step#1  pm(>>,forward)  area=8.07  rise=3.26 twist=35.7
  step#2  pm(>>,forward)  area=16.55 rise=3.38 twist=23.5
  step#3  pm(>>,forward)  area=12.16 rise=3.38 twist=27.0
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG4,A.DG5,A.DG6,A.DG7
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG10,A.DG11,A.DG12,A.DG13
  strand#3 DNA glyco-bond=---- sugar=--.- nts=4 GGGG A.DG16,A.DG17,A.DG18,A.DG19
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG22,A.DG23,A.DG24,A.DG25

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
  step#1  pm(>>,forward)  area=8.07  rise=3.26 twist=35.7

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3  glyco-bond=---- sugar=--.- groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG12,A.DG18,A.DG24
  step#2  pm(>>,forward)  area=16.55 rise=3.38 twist=23.5

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 3  glyco-bond=---- sugar=--.- groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG12,A.DG18,A.DG24
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG7,A.DG13,A.DG19,A.DG25
  step#3  pm(>>,forward)  area=12.16 rise=3.38 twist=27.0

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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, 4 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 4(-P-P-P)
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3  glyco-bond=---- sugar=--.- groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG12,A.DG18,A.DG24
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG7,A.DG13,A.DG19,A.DG25
  step#1  pm(>>,forward)  area=8.07  rise=3.26 twist=35.7
  step#2  pm(>>,forward)  area=16.55 rise=3.38 twist=23.5
  step#3  pm(>>,forward)  area=12.16 rise=3.38 twist=27.0
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG4,A.DG5,A.DG6,A.DG7
  strand#2  U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG10,A.DG11,A.DG12,A.DG13
  strand#3  U DNA glyco-bond=---- sugar=--.- nts=4 GGGG A.DG16,A.DG17,A.DG18,A.DG19
  strand#4  U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG22,A.DG23,A.DG24,A.DG25
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT8,A.DT9
  loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT14,A.DT15
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT20,A.DT21

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