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

PDB-id
2kzd
Class
DNA
Method
NMR
Summary
Structure of a (3+1) G-quadruplex formed by htert promoter sequence
Reference
Lim, K.W., Lacroix, L., Yue, D.J.E., Lim, J.K.C., Lim, J.M.W., Phan, A.T.: (2010) "Coexistence of two distinct G-quadruplex conformations in the hTERT promoter." J.Am.Chem.Soc., 132, 12331-12342.
Abstract
The catalytic subunit of human telomerase, hTERT, actively elongates the 3' end of the telomere in most cancer cells. The hTERT promoter, which contains many guanine-rich stretches on the same DNA strand, exhibits an exceptional potential for G-quadruplex formation. Here we show that one particular G-rich sequence in this region coexists in two G-quadruplex conformations in potassium solution: a (3 + 1) and a parallel-stranded G-quadruplexes. We present the NMR solution structures of both conformations, each comprising several robust structural elements, among which include the (3 + 1) and all-parallel G-tetrad cores, single-residue double-chain-reversal loops, and a capping A.T base pair. A combination of NMR and CD techniques, complemented with sequence modifications and variations of experimental condition, allowed us to better understand the coexistence of the two G-quadruplex conformations in equilibrium and how different structural elements conspire to favor a particular form.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-Lw-Ln-P), hybrid-2(3+1), UDUU

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=s-ss groove=wn-- planarity=0.209 type=other  nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17
 2 glyco-bond=-s-- groove=wn-- planarity=0.117 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18
 3 glyco-bond=-s-- groove=wn-- planarity=0.181 type=other  nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19

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=s-ss groove=wn-- Major-->WC nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17
 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18
 3  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
  step#1  mm(<>,outward)  area=11.40 rise=3.86 twist=21.6
  step#2  pm(>>,forward)  area=11.97 rise=3.19 twist=30.5
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-ss nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams
 1  glyco-bond=s-ss groove=wn-- Major-->WC nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17
2 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18
step#1 mm(<>,outward) area=11.40 rise=3.86 twist=21.6

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 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18
3 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
step#2 pm(>>,forward) area=11.97 rise=3.19 twist=30.5

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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, UDUU, anti-parallel, 3(-Lw-Ln-P), hybrid-2(3+1)

 1  glyco-bond=s-ss groove=wn-- Major-->WC nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17
 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18
 3  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
  step#1  mm(<>,outward)  area=11.40 rise=3.86 twist=21.6
  step#2  pm(>>,forward)  area=11.97 rise=3.19 twist=30.5
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-ss nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  U DNA glyco-bond=s-- nts=3 GGG A.DG17,A.DG18,A.DG19
  loop#1 type=lateral   strands=[#1,#2] nts=3 gAG A.DI5,A.DA6,A.DG7
  loop#2 type=lateral   strands=[#2,#3] nts=2 CT A.DC11,A.DT12
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA16

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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)