Summary information and primary citation

PDB-id
9p9y
Class
DNA
Method
NMR
Summary
Solution structure of the major pdgfrb promoter g-quadruplex with a broken-strand g21 fill-in
Reference
Han Y, Dickerhoff J, Yang D (2026): "Structures and dynamics of the major G-quadruplex in the human PDGFR-beta gene promoter: insights into vacancy G-quadruplex formation." Nucleic Acids Res., 54. doi: 10.1093/nar/gkag843.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-P-P-P)

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

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.182 type=other  O+ nts=4 GGGG X.DG3,X.DG7,X.DG11,X.DG14
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.330 type=bowl   O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG15
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.372 type=bowl   N+ nts=4 GGGG X.DG5,X.DG9,X.DG21,X.DG16

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG3,X.DG7,X.DG11,X.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG15
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG X.DG5,X.DG9,X.DG21,X.DG16
  step#1  pm(>>,forward)  area=13.23 rise=3.44 twist=25.0
  step#2  pm(>>,forward)  area=10.52 rise=3.47 twist=29.1
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG3,X.DG4,X.DG5
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG7,X.DG8,X.DG9
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG11,X.DG12,X.DG21
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG14,X.DG15,X.DG16

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG3,X.DG7,X.DG11,X.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG15
  step#1  pm(>>,forward)  area=13.23 rise=3.44 twist=25.0

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG15
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG X.DG5,X.DG9,X.DG21,X.DG16
  step#2  pm(>>,forward)  area=10.52 rise=3.47 twist=29.1

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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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG3,X.DG7,X.DG11,X.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG15
  step#1  pm(>>,forward)  area=13.23 rise=3.44 twist=25.0
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG X.DG3,X.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG X.DG7,X.DG8
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG X.DG11,X.DG12
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG X.DG14,X.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 GA X.DG5,X.DA6
  loop#2 type=propeller strands=[#2,#3] nts=2 GC X.DG9,X.DC10
  loop#3 type=propeller strands=[#3,#4] nts=1 C X.DC13

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List of 1 non-stem G4-loop (including the two closing Gs)

 1 type=lateral   helix=#1 nts=6 GGCAGG X.DG16,X.DG17,X.DC18,X.DA19,X.DG20,X.DG21