DSSR-curated G4 structure: PDB entry 7ecf

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

PyMOL session file	PDB file	View in 3Dmol.js

 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

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 Download PDB file Interactive view in 3Dmol.js
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 Download PDB file Interactive view in 3Dmol.js
	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 Download PDB file Interactive view in 3Dmol.js
	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 Download PDB file Interactive view in 3Dmol.js

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 Download PDB file Interactive view in 3Dmol.js
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 Download PDB file Interactive view in 3Dmol.js
	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 Download PDB file Interactive view in 3Dmol.js
	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 Download PDB file Interactive view in 3Dmol.js

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 Download PDB file Interactive view in 3Dmol.js
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 Download PDB file Interactive view in 3Dmol.js
	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 Download PDB file Interactive view in 3Dmol.js
	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 Download PDB file Interactive view in 3Dmol.js

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

Download PDB file
Interactive view in 3Dmol.js

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

Download PDB file
Interactive view in 3Dmol.js

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

Download PDB file
Interactive view in 3Dmol.js

Detailed DSSR results for the G-quadruplex: PDB entry 7ecf

Summary information

Base-block schematics in six views

List of 12 G-tetrads

List of 3 G4-helices

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

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

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

List of 3 G4-stems

Stem#1, 4 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

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

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