DSSR-enabled G4 identification/annotation: PDB entry 6jjf
Summary information and primary citation
- PDB-id
- 6jjf
- Class
- DNA
- Method
- X-ray (1.47 Å)
- Summary
- Crystal structure of a two-quartet DNA mixed-parallel-antiparallel g-quadruplex
- Reference
- Zhang Y, El Omari K, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D (2020): "Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths." Nucleic Acids Res., 48, 9886-9898. doi: 10.1093/nar/gkaa439.
- Abstract
- Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UDUD, anti-parallel:chair, 2+2; UUUU, parallel, 4+0, coaxial interfaces: mixed
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.186 type=saddle -- nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.254 type=bowl-2 -- nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 3 glyco-bond=---- sugar=---- groove=---- planarity=0.182 type=other -- nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12 4 glyco-bond=---- sugar=---- groove=---- planarity=0.253 type=other -- nts=4 GGGG A.DG10,A.DG13,B.DG10,B.DG13
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, inter-molecular, with 2 stems
|
1 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major -- nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 2* glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 3 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12 4 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG10,B.DG13,B.DG10,A.DG13 step#1 mm(<>,outward) area=19.57 rise=3.52 twist=11.6 step#2 pm(>>,forward) area=6.90 rise=3.21 twist=-38.1 step#3 pm(>>,forward) area=7.76 rise=3.26 twist=35.9 strand#1 DNA glyco-bond=-s-- sugar=---- nts=4 GGGG A.DG2,A.DG1,A.DG9,A.DG10 strand#2 DNA glyco-bond=s--- sugar=---- nts=4 GGGG A.DG6,A.DG7,B.DG12,B.DG13 strand#3 DNA glyco-bond=-s-- sugar=---- nts=4 GGGG B.DG2,B.DG1,B.DG9,B.DG10 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG B.DG6,B.DG7,A.DG12,A.DG13 |
| 3 stacking diagrams | |
|
1 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major -- nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 |
|
2* glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 |
|
3 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12 |
List of 2 G4-stems
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-tetrads, 2 loops, inter-molecular, UDUD, anti-parallel:chair, 2+2
|
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 2 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major -- nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 step#1 mm(<>,outward) area=19.57 rise=3.52 twist=11.6 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.DG7,A.DG6 strand#3 U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2 strand#4 D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG7,B.DG6 loop#1 type=lateral strands=[#1,#2] nts=3 CTC A.DC3,A.DT4,A.DC5 loop#2 type=lateral strands=[#3,#4] nts=3 CTC B.DC3,B.DT4,B.DC5 |
Stem#2, 2 G-tetrads, 2 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG10,A.DG13,B.DG10,B.DG13 step#1 pm(>>,forward) area=7.76 rise=3.26 twist=35.9 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG9,A.DG10 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG12,A.DG13 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG9,B.DG10 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG12,B.DG13 loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC11 loop#2 type=propeller strands=[#3,#4] nts=1 C B.DC11 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [mixed]