DSSR-enabled G4 identification/annotation: PDB entry 201d
Summary information and primary citation
- PDB-id
- 201d
- Class
- DNA
- Method
- NMR
- Summary
- Solution structure of the oxytricha telomeric repeat d[g4(t4g4)3] g-tetraplex
- Reference
- Wang Y, Patel DJ (1995): "Solution structure of the Oxytricha telomeric repeat d[G4(T4G4)3] G-tetraplex." J.Mol.Biol., 251, 76-94. doi: 10.1006/jmbi.1995.0417.
- Abstract
- The solution structure of Oxytricha telomere sequence d[G4(T4G4)3] in 0.1 M Na+ containing solution has been determined using a combined NMR-molecular dynamics approach including relaxation matrix refinement. This four G4 repeat sequence folds intramolecularly into a right-handed G-tetraplex containing four stacked G-tetrads which are connected by two lateral T4 loops and a central diagonal T4 loop. The guanine glycosidic bonds adopt a syn-anti alternation along the full length of the d[G4(T4G4)3] sequence while the orientation around adjacent G-tetrads switches between syn.syn.anti.anti and anti.anti.syn.syn alignments. Four distinct grooves are formed by the parallel (two of medium width) and anti-parallel (one wide and one narrow width) alignment of adjacent G-G-G-G segments in the G-tetraplex. The T4 residues in the diagonal loop are well-defined while the T4 residues in both lateral loops are under-defined and sample multiple conformations. The solution structure of the Na(+)-stabilized Oxytricha d[G4(T4G4)3] G-tetraplex and an earlier solution structure reported from our laboratory on the Na(+)-stabilized human d[AG3(T2AG3)3] G-tetraplex exhibit a common folding topology defined by the same syn/anti distribution of guanine residues along individual strands and around individual G-tetrads, as well as a common central diagonal loop which defines the strand directionalities. The well-resolved proton NMR spectra associated with the d[G4(T4G4)3] G-tetraplex opens the opportunity for studies ranging from cation-dependent characterization of G-tetraplex conformation and hydration to ligand and protein recognition of the distinct grooves associated with this folding topology.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2, 4(-LwD+Ln)
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=s--s sugar=-.-- groove=w-n- planarity=0.464 type=bowl N- nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.250 type=other N+ nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.205 type=other N- nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.290 type=other N+ nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
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-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=s--s sugar=-.-- groove=w-n- Major-->WC N- nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20 step#1 mm(<>,outward) area=11.71 rise=3.61 twist=19.1 step#2 pp(><,inward) area=17.57 rise=3.65 twist=37.2 step#3 mm(<>,outward) area=11.76 rise=3.75 twist=17.6 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=-s-s sugar=.--- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG28,A.DG27,A.DG26,A.DG25 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG17,A.DG18,A.DG19,A.DG20 |
| 3 stacking diagrams | |
|
1 glyco-bond=s--s sugar=-.-- groove=w-n- Major-->WC N- nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17 |
|
2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18 |
|
3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19 |
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, 4 G-tetrads, 3 loops, INTRA-molecular, UDDU, anti-parallel:basket, 2+2, 4(-LwD+Ln)
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1 glyco-bond=s--s sugar=-.-- groove=w-n- Major-->WC N- nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20 step#1 mm(<>,outward) area=11.71 rise=3.61 twist=19.1 step#2 pp(><,inward) area=17.57 rise=3.65 twist=37.2 step#3 mm(<>,outward) area=11.76 rise=3.75 twist=17.6 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 D DNA glyco-bond=-s-s sugar=.--- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG28,A.DG27,A.DG26,A.DG25 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG17,A.DG18,A.DG19,A.DG20 loop#1 type=lateral strands=[#1,#2] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT A.DT13,A.DT14,A.DT15,A.DT16 loop#3 type=lateral strands=[#4,#3] nts=4 TTTT A.DT21,A.DT22,A.DT23,A.DT24 |