Summary information

PDB id
4u5m
Class
DNA
Method
X-ray (1.5 Å)
Summary
Structure of a left-handed DNA g-quadruplex
Reference
Chung WJ, Heddi B, Schmitt E, Lim KW, Mechulam Y, Phan AT (2015): "Structure of a left-handed DNA G-quadruplex." Proc.Natl.Acad.Sci.USA, 112, 2729-2733. doi: 10.1073/pnas.1418718112.
Abstract
Aside from the well-known double helix, DNA can also adopt an alternative four-stranded structure known as G-quadruplex. Implications of such a structure in cellular processes, as well as its therapeutic and diagnostic applications, have been reported. The G-quadruplex structure is highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of a left-handed DNA G-quadruplex. The structure displays unprecedented features that can be exploited as unique recognition elements.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+P+P+P), parallel(4+0), UUUU, negative twist

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.219 type=other  nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.079 type=planar nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.088 type=planar nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.193 type=other  nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG26

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

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG24,A.DG15,A.DG18,A.DG21
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG23,A.DG26,A.DG17,A.DG20
  step#1  mp(<<,backward) area=10.88 rise=3.29 twist=-28.1
  step#2  mm(<>,outward)  area=29.32 rise=3.30 twist=-10.9
  step#3  pm(>>,forward)  area=12.02 rise=3.29 twist=-25.8
  strand#1 DNA glyco-bond=s--- sugar=---- nts=4 GGGG A.DG2,A.DG3,A.DG24,A.DG23
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG11,A.DG12,A.DG15,A.DG26
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG8,A.DG9,A.DG18,A.DG17
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG5,A.DG6,A.DG21,A.DG20

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3 stacking diagrams 
 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6
  step#1  mp(<<,backward) area=10.88 rise=3.29 twist=-28.1

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 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG24,A.DG15,A.DG18,A.DG21
  step#2  mm(<>,outward)  area=29.32 rise=3.30 twist=-10.9

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG24,A.DG15,A.DG18,A.DG21
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG23,A.DG26,A.DG17,A.DG20
  step#3  pm(>>,forward)  area=12.02 rise=3.29 twist=-25.8

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List of 1 G4-stem

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(+P+P+P), parallel(4+0)

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6
  step#1  mp(<<,backward) area=10.88 rise=3.29 twist=-28.1
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG2,A.DG3
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG11,A.DG12
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG5,A.DG6
  loop#1 type=propeller strands=[#1,#4] nts=1 T A.DT4
  loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT7
  loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT10

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List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=4 GTGG A.DG15,A.DT16,A.DG17,A.DG18
 2* type=V-shaped  helix=#1 nts=4 GGTG A.DG23,A.DG24,A.DT25,A.DG26