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PDB-id
6jkn
Class
DNA
Method
X-ray (1.4 Å)
Summary
Crystal structure of G-quadruplex formed by bromo-substituted human telomeric DNA
Reference
Geng, Y., Liu, C., Zhou, B., Cai, Q., Miao, H., Shi, X., Xu, N., You, Y., Fung, C.P., Din, R.U., Zhu, G.: (2019) "The crystal structure of an antiparallel chair-type G-quadruplex formed by Bromo-substituted human telomeric DNA." Nucleic Acids Res., 47, 5395-5404.
Abstract
Human telomeric guanine-rich DNA, which could adopt different G-quadruplex structures, plays important roles in protecting the cell from recombination and degradation. Although many of these structures were determined, the chair-type G-quadruplex structure remains elusive. Here, we present a crystal structure of the G-quadruplex composed of the human telomeric sequence d[GGGTTAGG8GTTAGGGTTAGG20G] with two dG to 8Br-dG substitutions at positions 8 and 20 with syn conformation in the K+ solution. It forms a novel three-layer chair-type G-quadruplex with two linking trinucleotide loops. Particularly, T5 and T17 are coplanar with two water molecules stacking on the G-tetrad layer in a sandwich-like mode through a coordinating K+ ion and an A6•A18 base pair. While a twisted Hoogsteen A12•T10 base pair caps on the top of G-tetrad core. The three linking TTA loops are edgewise and each DNA strand has two antiparallel adjacent strands. Our findings contribute to a deeper understanding and highlight the unique roles of loop and water molecule in the folding of the G-quadruplex.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-Lw-Ln-Lw), chair(2+2), UDUD

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=s-s- groove=wnwn planarity=0.607 type=bowl-2 nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2 glyco-bond=-s-s groove=wnwn planarity=0.531 type=saddle nts=4 GgGg A.DG2,A.BGM8,A.DG14,A.BGM20
 3 glyco-bond=-s-s groove=wnwn planarity=0.341 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19

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, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GgGg A.DG2,A.BGM8,A.DG14,A.BGM20
 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
  step#1  mm(<>,outward)  area=18.08 rise=3.57 twist=19.1
  step#2  pm(>>,forward)  area=16.06 rise=3.44 twist=25.0
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=-ss nts=3 GgG A.DG9,A.BGM8,A.DG7
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=-ss nts=3 GgG A.DG21,A.BGM20,A.DG19

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2 stacking diagrams
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
2 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GgGg A.DG2,A.BGM8,A.DG14,A.BGM20
step#1 mm(<>,outward) area=18.08 rise=3.57 twist=19.1

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 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GgGg A.DG2,A.BGM8,A.DG14,A.BGM20
3 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
step#2 pm(>>,forward) area=16.06 rise=3.44 twist=25.0

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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, 3 loops, INTRA-molecular, UDUD, anti-parallel, 3(-Lw-Ln-Lw), chair(2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GgGg A.DG2,A.BGM8,A.DG14,A.BGM20
 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
  step#1  mm(<>,outward)  area=18.08 rise=3.57 twist=19.1
  step#2  pm(>>,forward)  area=16.06 rise=3.44 twist=25.0
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss nts=3 GgG A.DG9,A.BGM8,A.DG7
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  D DNA glyco-bond=-ss nts=3 GgG A.DG21,A.BGM20,A.DG19
  loop#1 type=lateral   strands=[#1,#2] nts=3 TTA A.DT4,A.DT5,A.DA6
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA A.DT10,A.DT11,A.DA12
  loop#3 type=lateral   strands=[#3,#4] nts=3 TTA A.DT16,A.DT17,A.DA18

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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)