Summary information

PDB id
2kpr
Class
DNA
Method
NMR
Summary
Monomeric intronic human chl1 gene quadruplex DNA NMR, 17 structures
Reference
Kuryavyi V, Patel DJ (2010): "Solution Structure of a Unique G-Quadruplex Scaffold Adopted by a Guanosine-Rich Human Intronic Sequence." Structure, 18, 73-82. doi: 10.1016/j.str.2009.10.015.
Abstract
We report on the solution structure of an unprecedented intramolecular G-quadruplex formed by the guanosine-rich human chl1 intronic d(G(3)-N-G(4)-N(2)-G(4)-N-G(3)-N) 19-mer sequence in K(+)-containing solution. This G-quadruplex, composed of three stacked G-tetrads containing four syn guanines, represents a new folding topology with two unique conformational features. The first guanosine is positioned within the central G-tetrad, in contrast to all previous structures of unimolecular G-quadruplexes, where the first guanosine is part of an outermost G-tetrad. In addition, a V-shaped loop, spanning three G-tetrad planes, contains no bridging nucleotides. The G-quadruplex scaffold is stabilized by a T*G*A triple stacked over the G-tetrad at one end and an unpaired guanosine stacked over the G-tetrad at the other end. Finally, the chl1 intronic DNA G-quadruplex scaffold contains a guanosine base intercalated between an extended G-G step, a feature observed in common with the catalytic site of group I introns. This unique structural scaffold provides a highly specific platform for the future design of ligands specifically targeted to intronic G-quadruplex platforms.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwX+P), UD3(1+3), UDDD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.134 type=planar nts=4 GGGG A.DG1,A.DG6,A.DG17,A.DG13
 2 glyco-bond=-sss sugar=---. groove=w--n planarity=0.162 type=other  nts=4 GGGG A.DG2,A.DG5,A.DG16,A.DG12
 3 glyco-bond=-s-- sugar=-3-3 groove=wn-- planarity=0.133 type=planar nts=4 GGGG A.DG7,A.DG11,A.DG14,A.DG18

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

 1  glyco-bond=-sss sugar=---. groove=w--n WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG16,A.DG12
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG6,A.DG17,A.DG13
 3  glyco-bond=s--- sugar=3-3- groove=w--n Major-->WC nts=4 GGGG A.DG11,A.DG7,A.DG18,A.DG14
  step#1  mm(<>,outward)  area=12.69 rise=3.66 twist=18.5
  step#2  pm(>>,forward)  area=7.42  rise=3.29 twist=34.9
  strand#1 DNA glyco-bond=-ss sugar=--3 nts=3 GGG A.DG2,A.DG1,A.DG11
  strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG5,A.DG6,A.DG7
  strand#3 DNA glyco-bond=s-- sugar=--3 nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4 DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG12,A.DG13,A.DG14

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2 stacking diagrams 
 1  glyco-bond=-sss sugar=---. groove=w--n WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG16,A.DG12
 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG6,A.DG17,A.DG13
  step#1  mm(<>,outward)  area=12.69 rise=3.66 twist=18.5

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 2  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG6,A.DG17,A.DG13
 3  glyco-bond=s--- sugar=3-3- groove=w--n Major-->WC nts=4 GGGG A.DG11,A.DG7,A.DG18,A.DG14
  step#2  pm(>>,forward)  area=7.42  rise=3.29 twist=34.9

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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, UDDD, hybrid-(mixed), 2(-LwX+P), UD3(1+3)

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG6,A.DG17,A.DG13
 2  glyco-bond=-sss sugar=---. groove=w--n WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG16,A.DG12
  step#1  mm(<>,outward)  area=12.69 rise=3.66 twist=18.5
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG17,A.DG16
  strand#4  D DNA glyco-bond=-s sugar=-. nts=2 GG A.DG13,A.DG12
  loop#1 type=lateral   strands=[#1,#2] nts=2 GT A.DG3,A.DT4
  loop#2 type=diag-prop strands=[#2,#4] nts=5 GGAAG A.DG7,A.DG8,A.DA9,A.DA10,A.DG11
  loop#3 type=propeller strands=[#4,#3] nts=2 GT A.DG14,A.DT15

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

 1 type=lateral   helix=#1 nts=5 GGAAG A.DG7,A.DG8,A.DA9,A.DA10,A.DG11
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG11,A.DG12,A.DG13,A.DG14