Summary information

PDB id
7ecf
Class
DNA
Method
X-ray (1.6 Å)
Summary
Crystal structure of d(g4c2)2-ba in c2221 space group
Reference
Geng Y, Liu C, Cai Q, Luo Z, Miao H, Shi X, Xu N, Fung CP, Choy TT, Yan B, Li N, Qian P, Zhou B, Zhu G (2021): "Crystal structure of parallel G-quadruplex formed by the two-repeat ALS- and FTD-related GGGGCC sequence." Nucleic Acids Res., 49, 5881-5890. doi: 10.1093/nar/gkab302.
Abstract
The hexanucleotide repeat expansion, GGGGCC (G4C2), within the first intron of the C9orf72 gene is known to be the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The G4C2 repeat expansions, either DNA or RNA, are able to form G-quadruplexes which induce toxicity leading to ALS/FTD. Herein, we report a novel crystal structure of d(G4C2)2 that self-associates to form an eight-layer parallel tetrameric G-quadruplex. Two d(G4C2)2 associate together as a parallel dimeric G-quadruplex which folds into a tetramer via 5'-to-5' arrangements. Each dimer consists of four G-tetrads connected by two CC propeller loops. Especially, the 3'-end cytosines protrude out and form C·C+•C·C+/ C·C•C·C+ quadruple base pair or C•C·C+ triple base pair stacking on the dimeric block. Our work sheds light on the G-quadruplexes adopted by d(G4C2) and yields the invaluable structural details for the development of small molecules to tackle neurodegenerative diseases, ALS and FTD.
G4 notes
12 G-tetrads, 3 G4 helices, 3 G4 stems, parallel(4+0), UUUU

Base-block schematics in six views

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List of 12 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.102 type=planar nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.137 type=planar nts=4 GGGG A.DG2,A.DG8,B.DG2,B.DG8
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.183 type=bowl-2 nts=4 GGGG A.DG3,A.DG9,B.DG3,B.DG9
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.313 type=bowl   nts=4 GGGG A.DG4,A.DG10,B.DG4,B.DG10
 5 glyco-bond=---- sugar=--.- groove=---- planarity=0.069 type=planar nts=4 GGGG C.DG1,C.DG7,D.DG1,D.DG7
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.155 type=planar nts=4 GGGG C.DG2,C.DG8,D.DG2,D.DG8
 7 glyco-bond=---- sugar=---- groove=---- planarity=0.126 type=planar nts=4 GGGG C.DG3,C.DG9,D.DG3,D.DG9
 8 glyco-bond=---- sugar=---- groove=---- planarity=0.277 type=bowl   nts=4 GGGG C.DG4,C.DG10,D.DG4,D.DG10
 9 glyco-bond=---- sugar=---- groove=---- planarity=0.053 type=planar nts=4 GGGG E.DG1,E.DG7,F.DG1,F.DG7
10 glyco-bond=---- sugar=---- groove=---- planarity=0.114 type=planar nts=4 GGGG E.DG2,E.DG8,F.DG2,F.DG8
11 glyco-bond=---- sugar=---- groove=---- planarity=0.110 type=planar nts=4 GGGG E.DG3,E.DG9,F.DG3,F.DG9
12 glyco-bond=---- sugar=---- groove=---- planarity=0.277 type=bowl   nts=4 GGGG E.DG4,E.DG10,F.DG4,F.DG10

List of 3 G4-helices

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=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG2,B.DG8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG3,B.DG9
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG4,B.DG10
  step#1  pm(>>,forward)  area=8.54  rise=3.34 twist=32.5
  step#2  pm(>>,forward)  area=12.25 rise=3.32 twist=27.9
  step#3  pm(>>,forward)  area=10.31 rise=3.39 twist=28.6
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG7,A.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG1,B.DG2,B.DG3,B.DG4
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG7,B.DG8,B.DG9,B.DG10

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3 stacking diagrams
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG2,B.DG8
step#1 pm(>>,forward) area=8.54 rise=3.34 twist=32.5

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG2,B.DG8
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG3,B.DG9
step#2 pm(>>,forward) area=12.25 rise=3.32 twist=27.9

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG3,B.DG9
4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG4,B.DG10
step#3 pm(>>,forward) area=10.31 rise=3.39 twist=28.6

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

 1  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG7,D.DG1,D.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG8,D.DG2,D.DG8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG9,D.DG3,D.DG9
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG10,D.DG4,D.DG10
  step#1  pm(>>,forward)  area=7.89  rise=3.37 twist=33.4
  step#2  pm(>>,forward)  area=11.44 rise=3.30 twist=29.1
  step#3  pm(>>,forward)  area=10.81 rise=3.39 twist=27.9
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG1,C.DG2,C.DG3,C.DG4
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG7,C.DG8,C.DG9,C.DG10
  strand#3 DNA glyco-bond=---- sugar=.--- nts=4 GGGG D.DG1,D.DG2,D.DG3,D.DG4
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG7,D.DG8,D.DG9,D.DG10

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3 stacking diagrams
 1  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG7,D.DG1,D.DG7
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG8,D.DG2,D.DG8
step#1 pm(>>,forward) area=7.89 rise=3.37 twist=33.4

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG8,D.DG2,D.DG8
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG9,D.DG3,D.DG9
step#2 pm(>>,forward) area=11.44 rise=3.30 twist=29.1

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG9,D.DG3,D.DG9
4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG10,D.DG4,D.DG10
step#3 pm(>>,forward) area=10.81 rise=3.39 twist=27.9

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Helix#3, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG1,E.DG7,F.DG1,F.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG2,E.DG8,F.DG2,F.DG8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG3,E.DG9,F.DG3,F.DG9
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG4,E.DG10,F.DG4,F.DG10
  step#1  pm(>>,forward)  area=8.73  rise=3.32 twist=32.3
  step#2  pm(>>,forward)  area=12.48 rise=3.30 twist=28.0
  step#3  pm(>>,forward)  area=11.42 rise=3.41 twist=26.7
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG E.DG1,E.DG2,E.DG3,E.DG4
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG E.DG7,E.DG8,E.DG9,E.DG10
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG F.DG1,F.DG2,F.DG3,F.DG4
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG F.DG7,F.DG8,F.DG9,F.DG10

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3 stacking diagrams
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG1,E.DG7,F.DG1,F.DG7
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG2,E.DG8,F.DG2,F.DG8
step#1 pm(>>,forward) area=8.73 rise=3.32 twist=32.3

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG2,E.DG8,F.DG2,F.DG8
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG3,E.DG9,F.DG3,F.DG9
step#2 pm(>>,forward) area=12.48 rise=3.30 twist=28.0

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG3,E.DG9,F.DG3,F.DG9
4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG4,E.DG10,F.DG4,F.DG10
step#3 pm(>>,forward) area=11.42 rise=3.41 twist=26.7

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List of 3 G4-stems

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, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,B.DG2,B.DG8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG3,B.DG9
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG4,B.DG10
  step#1  pm(>>,forward)  area=8.54  rise=3.34 twist=32.5
  step#2  pm(>>,forward)  area=12.25 rise=3.32 twist=27.9
  step#3  pm(>>,forward)  area=10.31 rise=3.39 twist=28.6
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG7,A.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG1,B.DG2,B.DG3,B.DG4
  strand#4  U DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG7,B.DG8,B.DG9,B.DG10
  loop#1 type=propeller strands=[#1,#2] nts=2 CC A.DC5,A.DC6
  loop#2 type=propeller strands=[#3,#4] nts=2 CC B.DC5,B.DC6

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

 1  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG C.DG1,C.DG7,D.DG1,D.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG2,C.DG8,D.DG2,D.DG8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG9,D.DG3,D.DG9
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG10,D.DG4,D.DG10
  step#1  pm(>>,forward)  area=7.89  rise=3.37 twist=33.4
  step#2  pm(>>,forward)  area=11.44 rise=3.30 twist=29.1
  step#3  pm(>>,forward)  area=10.81 rise=3.39 twist=27.9
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG1,C.DG2,C.DG3,C.DG4
  strand#2  U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG7,C.DG8,C.DG9,C.DG10
  strand#3  U DNA glyco-bond=---- sugar=.--- nts=4 GGGG D.DG1,D.DG2,D.DG3,D.DG4
  strand#4  U DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG7,D.DG8,D.DG9,D.DG10
  loop#1 type=propeller strands=[#1,#2] nts=2 CC C.DC5,C.DC6
  loop#2 type=propeller strands=[#3,#4] nts=2 CC D.DC5,D.DC6

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Stem#3, 4 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG1,E.DG7,F.DG1,F.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG2,E.DG8,F.DG2,F.DG8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG3,E.DG9,F.DG3,F.DG9
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG4,E.DG10,F.DG4,F.DG10
  step#1  pm(>>,forward)  area=8.73  rise=3.32 twist=32.3
  step#2  pm(>>,forward)  area=12.48 rise=3.30 twist=28.0
  step#3  pm(>>,forward)  area=11.42 rise=3.41 twist=26.7
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG E.DG1,E.DG2,E.DG3,E.DG4
  strand#2  U DNA glyco-bond=---- sugar=---- nts=4 GGGG E.DG7,E.DG8,E.DG9,E.DG10
  strand#3  U DNA glyco-bond=---- sugar=---- nts=4 GGGG F.DG1,F.DG2,F.DG3,F.DG4
  strand#4  U DNA glyco-bond=---- sugar=---- nts=4 GGGG F.DG7,F.DG8,F.DG9,F.DG10
  loop#1 type=propeller strands=[#1,#2] nts=2 CC E.DC5,E.DC6
  loop#2 type=propeller strands=[#3,#4] nts=2 CC F.DC5,F.DC6

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