DSSR-derived G-quadruplex features in PDB entry 1jb7
- DNA-binding protein-DNA
- X-ray (1.86 Å)
- DNA G-quartets in a 1.86 a resolution structure of an oxytricha nova telomeric protein-DNA complex
- Horvath, M.P., Schultz, S.C.: (2001) "DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex." J.Mol.Biol., 310, 367-377.
- The Oxytricha nova telomere end binding protein (OnTEBP) recognizes, binds and protects the single-stranded 3'-terminal DNA extension found at the ends of macronuclear chromosomes. The structure of this complex shows that the single strand GGGGTTTTGGGG DNA binds in a deep cleft between the two protein subunits of OnTEBP, adopting a non-helical and irregular conformation. In extending the resolution limit of this structure to 1.86 A, we were surprised to find a G-quartet linked dimer of the GGGGTTTTGGGG DNA also packing within the crystal lattice and interacting with the telomere end binding protein. The G-quartet DNA exhibits the same structure and topology as previously observed in solution by NMR with diagonally crossing d(TTTT) loops at either end of the four-stranded helix. Additionally, the crystal structure reveals clearly visible Na(+), and specific patterns of bound water molecules in the four non-equivalent grooves. Although the G-quartet:protein contact surfaces are modest and might simply represent crystal packing interactions, it is interesting to speculate that the two types of telomeric DNA-protein interactions observed here might both be important in telomere biology.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDDU
1 glyco-bond=s--s groove=w-n- planarity=0.321 type=bowl nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9 2 glyco-bond=-ss- groove=w-n- planarity=0.168 type=other nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10 3 glyco-bond=s--s groove=w-n- planarity=0.157 type=planar nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11 4 glyco-bond=-ss- groove=w-n- planarity=0.287 type=bowl nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12
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, inter-molecular, with 1 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.