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

PDB-id
6n65
Class
DNA
Method
X-ray (1.6 Å)
Summary
Kras G-quadruplex g16t mutant
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=0.040 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2 glyco-bond=---- groove=---- planarity=0.127 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3 glyco-bond=---- groove=---- planarity=0.206 type=bowl   nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
 4 glyco-bond=---- groove=---- planarity=0.041 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=0.205 type=bowl   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=10.98 rise=3.38 twist=29.3
  step#2  mp(<<,backward) area=10.88 rise=3.43 twist=29.5
  step#3  mm(<>,outward)  area=28.28 rise=3.33 twist=-9.3
  step#4  pm(>>,forward)  area=10.06 rise=3.41 twist=30.1
  step#5  pm(>>,forward)  area=10.67 rise=3.40 twist=29.2
  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=10.98 rise=3.38 twist=29.3

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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=10.88 rise=3.43 twist=29.5

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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=28.28 rise=3.33 twist=-9.3

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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=10.06 rise=3.41 twist=30.1

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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=10.67 rise=3.40 twist=29.2

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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=10.88 rise=3.43 twist=29.5
  step#2  pm(>>,forward)  area=10.98 rise=3.38 twist=29.3
  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 T A.DT8
  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 AATA A.DA14,A.DA15,A.DT16,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=10.06 rise=3.41 twist=30.1
  step#2  pm(>>,forward)  area=10.67 rise=3.40 twist=29.2
  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 T B.DT8
  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 AATA B.DA14,B.DA15,B.DT16,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)