DSSR-curated G4 structure: PDB entry 6jji

Summary information

PDB id: 6jji
Class: RNA
Method: X-ray (3.1 Å)
Summary: Crystal structure of a two-quartet RNA parallel g-quadruplex complexed with the porphyrin tmpyp4 (1:1)
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, parallel(4+0), UUUU, coaxial interfaces: 3'/5'

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=ssss sugar=3333 groove=---- planarity=0.223 type=other  nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.179 type=bowl-2 nts=4 GGGG 1:B.G2,1:B.G7,2:B.G2,2:B.G7
 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.130 type=planar nts=4 GGGG 1:B.G9,1:B.G12,2:B.G9,2:B.G12
 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.184 type=other  nts=4 GGGG 1:B.G10,1:B.G13,2:B.G10,2:B.G13

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=ssss sugar=3333 groove=---- Major-->WC nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6 2* glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7 3 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:B.G12,2:B.G9,2:B.G12,1:B.G9 4 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:B.G13,2:B.G10,2:B.G13,1:B.G10 step#1 mp(<<,backward) area=6.43 rise=3.26 twist=-44.6 step#2 mm(<>,outward) area=27.73 rise=3.37 twist=-8.6 step#3 pm(>>,forward) area=9.27 rise=3.20 twist=32.6 strand#1 RNA glyco-bond=s--- sugar=3-33 nts=4 GGGG 1:B.G1,1:B.G2,1:B.G12,1:B.G13 strand#2 RNA glyco-bond=s--- sugar=3--- nts=4 GGGG 2:B.G6,2:B.G7,2:B.G9,2:B.G10 strand#3 RNA glyco-bond=s--- sugar=3-33 nts=4 GGGG 2:B.G1,2:B.G2,2:B.G12,2:B.G13 strand#4 RNA glyco-bond=s--- sugar=3--- nts=4 GGGG 1:B.G6,1:B.G7,1:B.G9,1:B.G10 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=ssss sugar=3333 groove=---- Major-->WC nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6 2* glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7 step#1 mp(<<,backward) area=6.43 rise=3.26 twist=-44.6 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7 3 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:B.G12,2:B.G9,2:B.G12,1:B.G9 step#2 mm(<>,outward) area=27.73 rise=3.37 twist=-8.6 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:B.G12,2:B.G9,2:B.G12,1:B.G9 4 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:B.G13,2:B.G10,2:B.G13,1:B.G10 step#3 pm(>>,forward) area=9.27 rise=3.20 twist=32.6 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, UUUU, parallel, parallel(4+0)

 1  glyco-bond=ssss sugar=3333 groove=---- Major-->WC nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7
  step#1  mp(<<,backward) area=6.43  rise=3.26 twist=-44.6
  strand#1  U RNA glyco-bond=s- sugar=3- nts=2 GG 1:B.G1,1:B.G2
  strand#2  U RNA glyco-bond=s- sugar=3- nts=2 GG 2:B.G6,2:B.G7
  strand#3  U RNA glyco-bond=s- sugar=3- nts=2 GG 2:B.G1,2:B.G2
  strand#4  U RNA glyco-bond=s- sugar=3- nts=2 GG 1:B.G6,1:B.G7
  loop#1 type=propeller strands=[#1,#4] nts=3 CUC 1:B.C3,1:B.U4,1:B.C5
  loop#2 type=propeller strands=[#3,#2] nts=3 CUC 2:B.C3,2:B.U4,2:B.C5

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG 1:B.G9,1:B.G12,2:B.G9,2:B.G12
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG 1:B.G10,1:B.G13,2:B.G10,2:B.G13
  step#1  pm(>>,forward)  area=9.27  rise=3.20 twist=32.6
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG 1:B.G9,1:B.G10
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG 1:B.G12,1:B.G13
  strand#3  U RNA glyco-bond=-- sugar=-- nts=2 GG 2:B.G9,2:B.G10
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG 2:B.G12,2:B.G13
  loop#1 type=propeller strands=[#1,#2] nts=1 C 1:B.C11
  loop#2 type=propeller strands=[#3,#4] nts=1 C 2:B.C11