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

PDB-id
6wck
Class
DNA
Method
X-ray (1.8 Å)
Summary
Kras G-quadruplex g16t mutant with bromo uracil replacing t8 and t16
Reference
Ou, A., Schmidberger, J.W., Wilson, K.A., Evans, C.W., Hargreaves, J.A., Grigg, M., O'Mara, M.L., Iyer, K.S., Bond, C.S., Smith, N.M.: (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.
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 · 3(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

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

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

List of 1 G4-helix [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, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG6,B.DG2,B.DG18
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG12,B.DG7,B.DG3,B.DG19
 6  glyco-bond=---- groove=---- Major-->WC 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=------ nts=6 GGGGGG A.DG4,A.DG3,A.DG2,B.DG11,B.DG12,B.DG13
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG A.DG9,A.DG7,A.DG6,B.DG6,B.DG7,B.DG9
  strand#3 DNA glyco-bond=------ nts=6 GGGGGG A.DG13,A.DG12,A.DG11,B.DG2,B.DG3,B.DG4
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG A.DG20,A.DG19,A.DG18,B.DG18,B.DG19,B.DG20

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
step#1 mp(<<,backward) area=11.14 rise=3.37 twist=29.4

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
step#2 mp(<<,backward) area=10.54 rise=3.37 twist=29.8

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG6,B.DG2,B.DG18
step#3 mm(<>,outward) area=28.56 rise=3.39 twist=-9.7

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG6,B.DG2,B.DG18
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG12,B.DG7,B.DG3,B.DG19
step#4 pm(>>,forward) area=10.30 rise=3.35 twist=30.3

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG12,B.DG7,B.DG3,B.DG19
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG13,B.DG9,B.DG4,B.DG20
step#5 pm(>>,forward) area=11.03 rise=3.38 twist=29.0

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3  glyco-bond=---- groove=---- WC-->Major 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=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2* U DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG9 bulged-nts=1 u A.BRU8
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=--- 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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Stem#2, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG18
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG19
 3  glyco-bond=---- groove=---- WC-->Major 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=--- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2* U DNA glyco-bond=--- nts=3 GGG B.DG6,B.DG7,B.DG9 bulged-nts=1 u B.BRU8
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- 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

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

List of 0 non-stem G4-loops (including the two closing Gs)