Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
3qxr
Class
DNA
Method
X-ray (1.62 Å)
Summary
Crystal structure of the brominated ckit-1 proto-oncogene promoter quadruplex DNA
Reference
Wei, D., Parkinson, G.N., Reszka, A.P., Neidle, S.: (2012) "Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation." Nucleic Acids Res., 40, 4691-4700.
Abstract
We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.
G4 notes
6 G-tetrads, 2 G4 helices, 2 G4 stems · 2(-PX+P), parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.230 type=other  nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13
 2 glyco-bond=---- groove=---- planarity=0.272 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 3 glyco-bond=---- groove=---- planarity=0.393 type=bowl   nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
 4 glyco-bond=---- groove=---- planarity=0.229 type=other  nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
 5 glyco-bond=---- groove=---- planarity=0.253 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 6 glyco-bond=---- groove=---- planarity=0.346 type=bowl   nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15

List of 2 G4-helices [summary · schematics · tetrads · stems · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
  step#1  pm(>>,forward)  area=10.90 rise=3.40 twist=29.0
  step#2  pm(>>,forward)  area=8.55  rise=3.39 twist=32.5
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG10,A.DG21,A.DG22
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG13,A.DG14,A.DG15

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
step#1 pm(>>,forward) area=10.90 rise=3.40 twist=29.0

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
step#2 pm(>>,forward) area=8.55 rise=3.39 twist=32.5

Download PDB file
Interactive view in 3Dmol.js

Helix#2, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
  step#1  pm(>>,forward)  area=10.28 rise=3.42 twist=30.2
  step#2  pm(>>,forward)  area=8.64  rise=3.39 twist=33.6
  strand#1 DNA glyco-bond=--- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2 DNA glyco-bond=--- nts=3 GGG B.DG6,B.DG7,B.DG8
  strand#3 DNA glyco-bond=--- nts=3 GGG B.DG10,B.DG21,B.DG22
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG13,B.DG14,B.DG15

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
step#1 pm(>>,forward) area=10.28 rise=3.42 twist=30.2

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
step#2 pm(>>,forward) area=8.64 rise=3.39 twist=33.6

Download PDB file
Interactive view in 3Dmol.js

List of 2 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

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, UUUU, parallel, 2(-PX+P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
  step#1  pm(>>,forward)  area=8.55  rise=3.39 twist=32.5
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG21,A.DG22
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG A.DA5,A.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCuG A.DC9,A.DG10,A.DC11,A.BRU12,A.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG A.DA16,A.DG17,A.DG18,A.DA19,A.DG20

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
  step#1  pm(>>,forward)  area=8.64  rise=3.39 twist=33.6
  strand#1  U DNA glyco-bond=-- nts=2 GG B.DG3,B.DG4
  strand#2  U DNA glyco-bond=-- nts=2 GG B.DG7,B.DG8
  strand#3  U DNA glyco-bond=-- nts=2 GG B.DG21,B.DG22
  strand#4  U DNA glyco-bond=-- nts=2 GG B.DG14,B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG B.DA5,B.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCuG B.DC9,B.DG10,B.DC11,B.BRU12,B.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG B.DA16,B.DG17,B.DG18,B.DA19,B.DG20

Download PDB file
Interactive view in 3Dmol.js

List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 4 non-stem G4-loops (including the two closing Gs)

 1* type=V-shaped  helix=#1 nts=5 GGGCG A.DG6,A.DG7,A.DG8,A.DC9,A.DG10
 2 type=lateral   helix=#1 nts=4 GCuG A.DG10,A.DC11,A.BRU12,A.DG13
 3* type=V-shaped  helix=#2 nts=5 GGGCG B.DG6,B.DG7,B.DG8,B.DC9,B.DG10
 4 type=lateral   helix=#2 nts=4 GCuG B.DG10,B.DC11,B.BRU12,B.DG13