DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 6wck
Class: DNA
Method: X-ray (1.801 Å)
Summary: Kras g-quadruplex g16t mutant with bromo uracil replacing t8 and t16.
Reference: Ou A, Schmidberger JW, Wilson KA, Evans CW, Hargreaves JA, Grigg M, O'Mara ML, Iyer KS, Bond CS, Smith NM (2020): "High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A pi-stacking interactions for small-molecule recognition." Nucleic Acids Res., 48, 5766-5776. doi: 10.1093/nar/gkaa262.
Abstract: Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 Å) of a KRAS G-quadruplex as a 5'-head-to-head dimer with extensive poly-A π-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A π-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indicated the poly-A loop was a binding site for these ligands in addition to the 5'-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of specific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 3(-P-P-P), coaxial interfaces: 5'/5'

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

List of 6 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.070 type=planar O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2 glyco-bond=---- sugar=-3-- groove=---- planarity=0.119 type=planar O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.184 type=other  O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.051 type=planar O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG18
 5 glyco-bond=---- sugar=-3-- groove=---- planarity=0.121 type=planar O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG19
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.198 type=other  O+ nts=4 GGGG B.DG4,B.DG9,B.DG13,B.DG20

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, 6 G-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20 2 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3* glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG11,B.DG6,B.DG2,B.DG18 5 glyco-bond=---- sugar=-3-- groove=---- Major-->WC O+ nts=4 GGGG B.DG12,B.DG7,B.DG3,B.DG19 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG13,B.DG9,B.DG4,B.DG20 step#1 mp(<<,backward) area=11.14 rise=3.37 twist=29.4 step#2 mp(<<,backward) area=10.54 rise=3.37 twist=29.8 step#3 mm(<>,outward) area=28.56 rise=3.39 twist=-9.7 step#4 pm(>>,forward) area=10.30 rise=3.35 twist=30.3 step#5 pm(>>,forward) area=11.03 rise=3.38 twist=29.0 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG4,A.DG3,A.DG2,B.DG11,B.DG12,B.DG13 strand#2 DNA glyco-bond=------ sugar=-3--3- nts=6 GGGGGG A.DG9,A.DG7,A.DG6,B.DG6,B.DG7,B.DG9 strand#3 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG13,A.DG12,A.DG11,B.DG2,B.DG3,B.DG4 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG20,A.DG19,A.DG18,B.DG18,B.DG19,B.DG20 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20 2 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 step#1 mp(<<,backward) area=11.14 rise=3.37 twist=29.4 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3* glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 step#2 mp(<<,backward) area=10.54 rise=3.37 twist=29.8 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG11,B.DG6,B.DG2,B.DG18 step#3 mm(<>,outward) area=28.56 rise=3.39 twist=-9.7 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG11,B.DG6,B.DG2,B.DG18 5 glyco-bond=---- sugar=-3-- groove=---- Major-->WC O+ nts=4 GGGG B.DG12,B.DG7,B.DG3,B.DG19 step#4 pm(>>,forward) area=10.30 rise=3.35 twist=30.3 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=-3-- groove=---- Major-->WC O+ nts=4 GGGG B.DG12,B.DG7,B.DG3,B.DG19 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG13,B.DG9,B.DG4,B.DG20 step#5 pm(>>,forward) area=11.03 rise=3.38 twist=29.0 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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, UUUU, parallel, 4+0, 3(-P-P-P)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2  glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
  step#1  pm(>>,forward)  area=10.54 rise=3.37 twist=29.8
  step#2  pm(>>,forward)  area=11.14 rise=3.37 twist=29.4
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2* U DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG6,A.DG7,A.DG9 bulged-nts=1 u A.BRU8
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC5
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT10
  loop#3 type=propeller strands=[#3,#4] nts=4 AAuA A.DA14,A.DA15,A.BRU16,A.DA17

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Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG18
 2  glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG19
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.DG4,B.DG9,B.DG13,B.DG20
  step#1  pm(>>,forward)  area=10.30 rise=3.35 twist=30.3
  step#2  pm(>>,forward)  area=11.03 rise=3.38 twist=29.0
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2* U DNA glyco-bond=--- sugar=-3- nts=3 GGG B.DG6,B.DG7,B.DG9 bulged-nts=1 u B.BRU8
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG18,B.DG19,B.DG20
  loop#1 type=propeller strands=[#1,#2] nts=1 C B.DC5
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT10
  loop#3 type=propeller strands=[#3,#4] nts=4 AAuA B.DA14,B.DA15,B.BRU16,B.DA17