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

PDB-id
2lod
Class
DNA
Method
NMR
Summary
Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops
Reference
Marusic, M., Sket, P., Bauer, L., Viglasky, V., Plavec, J.: (2012) "Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops." Nucleic Acids Res., 40, 6946-6956.
Abstract
We herein report on the formation and high-resolution NMR solution-state structure determination of a G-quadruplex adopted by d[G(3)ATG(3)ACACAG(4)ACG(3)] comprised of four G-tracts with the third one consisting of four guanines that are intervened with non-G streches of different lengths. A single intramolecular antiparallel (3+1) G-quadruplex exhibits three stacked G-quartets connected with propeller, diagonal and edgewise loops of different lengths. The propeller and edgewise loops are well structured, whereas the longer diagonal loop is more flexible. To the best of our knowledge, this is the first high-resolution G-quadruplex structure where all of the three main loop types are present.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-PD+Lw), U3D(3+1), UUUD

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

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=sss- groove=--wn planarity=0.219 type=other  nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16
 2 glyco-bond=---s groove=--wn planarity=0.109 type=planar nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
 3 glyco-bond=---s groove=--wn planarity=0.309 type=bowl   nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14

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, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
 3  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14
  step#1  mm(<>,outward)  area=15.30 rise=3.50 twist=17.7
  step#2  pm(>>,forward)  area=13.84 rise=3.45 twist=25.1
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG20,A.DG21,A.DG22
  strand#4 DNA glyco-bond=-ss nts=3 GGG A.DG16,A.DG15,A.DG14

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2 stacking diagrams
 1  glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
step#1 mm(<>,outward) area=15.30 rise=3.50 twist=17.7

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 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14
step#2 pm(>>,forward) area=13.84 rise=3.45 twist=25.1

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List of 1 G4-stem [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, UUUD, anti-parallel, 3(-PD+Lw), U3D(3+1)

 1  glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
 3  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14
  step#1  mm(<>,outward)  area=15.30 rise=3.50 twist=17.7
  step#2  pm(>>,forward)  area=13.84 rise=3.45 twist=25.1
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG20,A.DG21,A.DG22
  strand#4  D DNA glyco-bond=-ss nts=3 GGG A.DG16,A.DG15,A.DG14
  loop#1 type=propeller strands=[#1,#2] nts=2 AT A.DA4,A.DT5
  loop#2 type=diagonal  strands=[#2,#4] nts=5 ACACA A.DA9,A.DC10,A.DA11,A.DC12,A.DA13
  loop#3 type=lateral   strands=[#4,#3] nts=3 GAC A.DG17,A.DA18,A.DC19

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

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