Summary information

PDB id
7atz
Class
DNA
Method
NMR
Summary
G-quadruplex with v-shaped loop from the first repeat of kcnn4 minisatellite
Reference
Vianney YM, Weisz K (2021): "First Tandem Repeat of a Potassium Channel KCNN4 Minisatellite Folds into a V-Loop G-Quadruplex Structure." Biochemistry, 60, 1337-1346. doi: 10.1021/acs.biochem.1c00043.
Abstract
The KCNN4 gene encoding a potassium channel protein whose expression has been correlated with tumor progression was found to comprise a guanine-rich minisatellite region with the ability to form a putative G-quadruplex (G4). Given the suggested regulatory role of G4s in gene expression, G-quadruplex formation for the polymorphic first repeat of the minisatellite was studied by nuclear magnetic resonance spectroscopy. A stable G-quadruplex of a truncated mutant sequence was shown to represent one of several coexisting species of the wild-type sequence. The high-resolution structure features a noncanonical G4 with a broken G-column and a V-shaped loop. The presence of a 3'-flanking thymidine interacting with the lateral loop preceding the V loop seems to be critical for the formation of this G4 topology. On the contrary, an additional 5'-flanking residue disfavored but still allowed folding into the V-loop structure. The latter may therefore serve as a putative therapeutic target in strategies for G4-based modulation of KCNN4 expression.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwX+P), UD3(1+3), UDDD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.216 type=other  nts=4 GGGG A.DG1,A.DG9,A.DG21,A.DG16
 2 glyco-bond=-ss- sugar=---3 groove=w-n- planarity=0.268 type=other  nts=4 GGGG A.DG2,A.DG8,A.DG20,A.DG15
 3 glyco-bond=-s-- sugar=-3-- groove=wn-- planarity=0.211 type=other  nts=4 GGGG A.DG10,A.DG14,A.DG17,A.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, INTRA-molecular, with 1 stem

 1  glyco-bond=-ss- sugar=---3 groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG20,A.DG15
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG21,A.DG16
 3  glyco-bond=s--- sugar=3--- groove=w--n Major-->WC nts=4 GGGG A.DG14,A.DG10,A.DG22,A.DG17
  step#1  mm(<>,outward)  area=10.07 rise=3.47 twist=22.5
  step#2  pm(>>,forward)  area=12.12 rise=3.28 twist=32.2
  strand#1 DNA glyco-bond=-ss sugar=--3 nts=3 GGG A.DG2,A.DG1,A.DG14
  strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22
  strand#4 DNA glyco-bond=--- sugar=3-- nts=3 GGG A.DG15,A.DG16,A.DG17

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2 stacking diagrams 
 1  glyco-bond=-ss- sugar=---3 groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG20,A.DG15
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG21,A.DG16
  step#1  mm(<>,outward)  area=10.07 rise=3.47 twist=22.5

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 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG21,A.DG16
 3  glyco-bond=s--- sugar=3--- groove=w--n Major-->WC nts=4 GGGG A.DG14,A.DG10,A.DG22,A.DG17
  step#2  pm(>>,forward)  area=12.12 rise=3.28 twist=32.2

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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-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 2(-LwX+P), UD3(1+3)

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG21,A.DG16
 2  glyco-bond=-ss- sugar=---3 groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG20,A.DG15
  step#1  mm(<>,outward)  area=10.07 rise=3.47 twist=22.5
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG9,A.DG8
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG21,A.DG20
  strand#4  D DNA glyco-bond=-- sugar=-3 nts=2 GG A.DG16,A.DG15
  loop#1 type=lateral   strands=[#1,#2] nts=5 TCTGA A.DT3,A.DC4,A.DT5,A.DG6,A.DA7
  loop#2 type=diag-prop strands=[#2,#4] nts=5 GAGAG A.DG10,A.DA11,A.DG12,A.DA13,A.DG14
  loop#3 type=propeller strands=[#4,#3] nts=3 GCT A.DG17,A.DC18,A.DT19

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List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=5 GAGAG A.DG10,A.DA11,A.DG12,A.DA13,A.DG14
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG14,A.DG15,A.DG16,A.DG17