DSSR-enabled G4 identification/annotation: PDB entry 2kzd
Summary information and primary citation
- PDB-id
- 2kzd
- Class
- DNA
- Method
- NMR
- Summary
- Structure of a (3+1) g-quadruplex formed by htert promoter sequence
- Reference
- Lim KW, Lacroix L, Yue DJE, Lim JKC, Lim JMW, Phan AT (2010): "Coexistence of two distinct G-quadruplex conformations in the hTERT promoter." J.Am.Chem.Soc., 132, 12331-12342. doi: 10.1021/ja101252n.
- 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, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=s-ss sugar=---- groove=wn-- planarity=0.209 type=other O- nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17 2 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.117 type=planar O+ nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18 3 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.181 type=other O+ nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
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-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ 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-- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG17,A.DG18,A.DG19 |
| 2 stacking diagrams | |
|
1 glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17 |
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2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18 |
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, 3 G-tetrads, 3 loops, INTRA-molecular, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)
|
1 glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG10,A.DG13,A.DG17 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG9,A.DG14,A.DG18 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ 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-- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8 strand#3 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 U DNA glyco-bond=s-- sugar=--- 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 |