Summary information

PDB id
8x1v
Class
DNA
Method
NMR
Summary
NMR structure of a bimolecular parallel g-quadruplex formed by aaggg repeats from pathogenic rfc1 gene
Reference
Wang Y, Guo P, Han D: "Structural Investigation of Pathogenic RFC1 AAGGG Pentanucleotide Repeats Reveals a Role of G-Quadruplex in Dysregulated Gene Expression in CANVAS."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---. groove=---- planarity=0.322 type=saddle nts=4 GGGG A.DG3,A.DG8,B.DG15,B.DG20
 2 glyco-bond=---- sugar=---3 groove=---- planarity=0.215 type=other  nts=4 GGGG A.DG4,A.DG9,B.DG16,B.DG21
 3 glyco-bond=---- sugar=--.. groove=---- planarity=0.183 type=other  nts=4 GGGG A.DG5,A.DG10,B.DG17,B.DG22

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, 3 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,B.DG15,B.DG20
 2  glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,B.DG16,B.DG21
 3  glyco-bond=---- sugar=--.. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG10,B.DG17,B.DG22
  step#1  pm(>>,forward)  area=7.80  rise=3.41 twist=35.0
  step#2  pm(>>,forward)  area=18.21 rise=3.31 twist=20.5
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=--- sugar=--. nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4 DNA glyco-bond=--- sugar=.3. nts=3 GGG B.DG20,B.DG21,B.DG22

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2 stacking diagrams
 1  glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,B.DG15,B.DG20
2 glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,B.DG16,B.DG21
step#1 pm(>>,forward) area=7.80 rise=3.41 twist=35.0

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 2  glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,B.DG16,B.DG21
3 glyco-bond=---- sugar=--.. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG10,B.DG17,B.DG22
step#2 pm(>>,forward) area=18.21 rise=3.31 twist=20.5

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

 1  glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,B.DG15,B.DG20
 2  glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,B.DG16,B.DG21
 3  glyco-bond=---- sugar=--.. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG10,B.DG17,B.DG22
  step#1  pm(>>,forward)  area=7.80  rise=3.41 twist=35.0
  step#2  pm(>>,forward)  area=18.21 rise=3.31 twist=20.5
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=--- sugar=--. nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4  U DNA glyco-bond=--- sugar=.3. nts=3 GGG B.DG20,B.DG21,B.DG22
  loop#1 type=propeller strands=[#1,#2] nts=2 AA A.DA6,A.DA7
  loop#2 type=propeller strands=[#3,#4] nts=2 AA B.DA18,B.DA19

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