Summary information and primary citation

PDB-id
9pa0
Class
DNA
Method
NMR
Summary
Hybrid-1 form of human telomere DNA quadruplex with wild-type 5'-flanking in k+ solution
Reference
Dickerhoff J, Yang D (2026): "NMR structure study of DNA G-quadruplexes and ligand complexes." Prog.Nucl.Magn.Reson. Spectros., 154-155, 101597. doi: 10.1016/j.pnmrs.2026.101597.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)

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

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List of 3 G-tetrads

 1 glyco-bond=ss-s sugar=---- groove=-wn- planarity=0.234 type=other  O- nts=4 GGGG X.DG4,X.DG10,X.DG18,X.DG22
 2 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.251 type=other  O+ nts=4 GGGG X.DG5,X.DG11,X.DG17,X.DG23
 3 glyco-bond=--s- sugar=-3-- groove=-wn- planarity=0.262 type=other  O+ nts=4 GGGG X.DG6,X.DG12,X.DG16,X.DG24

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=ss-s sugar=---- groove=-wn- Major-->WC O- nts=4 GGGG X.DG4,X.DG10,X.DG18,X.DG22
 2  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG X.DG5,X.DG11,X.DG17,X.DG23
 3  glyco-bond=--s- sugar=-3-- groove=-wn- WC-->Major O+ nts=4 GGGG X.DG6,X.DG12,X.DG16,X.DG24
  step#1  mm(<>,outward)  area=19.50 rise=3.54 twist=11.6
  step#2  pm(>>,forward)  area=14.32 rise=3.39 twist=26.1
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6
  strand#2 DNA glyco-bond=s-- sugar=--3 nts=3 GGG X.DG10,X.DG11,X.DG12
  strand#3 DNA glyco-bond=-ss sugar=--- nts=3 GGG X.DG18,X.DG17,X.DG16
  strand#4 DNA glyco-bond=s-- sugar=--- nts=3 GGG X.DG22,X.DG23,X.DG24

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2 stacking diagrams 
 1  glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC O- nts=4 GGGG X.DG4,X.DG10,X.DG18,X.DG22
 2  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG X.DG5,X.DG11,X.DG17,X.DG23
  step#1  mm(<>,outward)  area=19.50 rise=3.54 twist=11.6

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 2  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG X.DG5,X.DG11,X.DG17,X.DG23
 3  glyco-bond=--s- sugar=-3-- groove=-wn- WC-->Major O+ nts=4 GGGG X.DG6,X.DG12,X.DG16,X.DG24
  step#2  pm(>>,forward)  area=14.32 rise=3.39 twist=26.1

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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, 3 G-tetrads, 3 loops, INTRA-molecular, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)
 1  glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC O- nts=4 GGGG X.DG4,X.DG10,X.DG18,X.DG22
 2  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG X.DG5,X.DG11,X.DG17,X.DG23
 3  glyco-bond=--s- sugar=-3-- groove=-wn- WC-->Major O+ nts=4 GGGG X.DG6,X.DG12,X.DG16,X.DG24
  step#1  mm(<>,outward)  area=19.50 rise=3.54 twist=11.6
  step#2  pm(>>,forward)  area=14.32 rise=3.39 twist=26.1
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6
  strand#2  U DNA glyco-bond=s-- sugar=--3 nts=3 GGG X.DG10,X.DG11,X.DG12
  strand#3  D DNA glyco-bond=-ss sugar=--- nts=3 GGG X.DG18,X.DG17,X.DG16
  strand#4  U DNA glyco-bond=s-- sugar=--- nts=3 GGG X.DG22,X.DG23,X.DG24
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA X.DT7,X.DT8,X.DA9
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA X.DT13,X.DT14,X.DA15
  loop#3 type=lateral   strands=[#3,#4] nts=3 TTA X.DT19,X.DT20,X.DA21

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