DSSR-curated G4 structure: PDB entry 6jjf

Summary information

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, (2+2), UDUD; parallel(4+0), UUUU, coaxial interfaces: mixed

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

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-tetrad layers, 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 Download PDB file Interactive view in 3Dmol.js
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 step#1 mm(<>,outward) area=19.57 rise=3.52 twist=11.6 Download PDB file Interactive view in 3Dmol.js
	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 step#2 pm(>>,forward) area=6.90 rise=3.21 twist=-38.1 Download PDB file Interactive view in 3Dmol.js
	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#3 pm(>>,forward) area=7.76 rise=3.26 twist=35.9 Download PDB file Interactive view in 3Dmol.js

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-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (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

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Interactive view in 3Dmol.js

Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, 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