DSSR-curated G4 structure: PDB entry 1n7b

Summary information

PDB id: 1n7b
Class: DNA, RNA
Method: X-ray (1.4 Å)
Summary: Rip-radiation-damage induced phasing
Reference: Ravelli RBG, Leiros H-KS, Pan B, Caffrey M, McSweeney S (2003): "Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures." Structure, 11, 217-224. doi: 10.1016/S0969-2126(03)00006-6.
Abstract: The use of third generation synchrotron sources has led to renewed concern about the effect of ionizing radiation on crystalline biological samples. In general, the problem is seen as one to be avoided. However, in this paper, it is shown that, far from being a hindrance to successful structure determination, radiation damage provides an opportunity for phasing macromolecular structures. This is successfully demonstrated for both a protein and an oligonucleotide, by way of which complete models were built automatically. The possibility that, through the exploitation of radiation damage, the phase problem could become less of a barrier to macromolecular crystal structure determination is discussed.
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, parallel(4+0), UUUU, coaxial interfaces: 5'/5'-SEPARATED

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.098 type=planar nts=4 gggg A.BGM2,C.BGM2,H.BGM2,D.BGM2
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.151 type=planar nts=4 GGGG A.G4,C.G4,H.G4,D.G4
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.264 type=bowl   nts=4 GGGG A.G5,C.G5,H.G5,D.G5
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.082 type=planar nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.154 type=planar nts=4 GGGG B.G4,E.G4,F.G4,G.G4
 6 glyco-bond=---- sugar=3333 groove=---- planarity=0.257 type=bowl   nts=4 GGGG B.G5,E.G5,F.G5,G.G5

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, 6 G-tetrad layers, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4 6 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G5,G.G5,F.G5,E.G5 step#1 mp(<<,backward) area=14.18 rise=3.64 twist=21.9 step#2 mp(<<,backward) area=0.00 rise=6.68 twist=149.2 step#3 mm(<>,outward) area=31.43 rise=3.40 twist=-15.3 step#4 pm(>>,forward) area=0.00 rise=6.67 twist=-31.2 step#5 pm(>>,forward) area=13.66 rise=3.62 twist=22.6 strand#1 RNA glyco-bond=------ sugar=33--33 nts=6 GGggGG A.G5,A.G4,A.BGM2,B.BGM2,B.G4,B.G5 strand#2 RNA glyco-bond=------ sugar=33--33 nts=6 GGggGG C.G5,C.G4,D.BGM2,E.BGM2,G.G4,G.G5 strand#3 RNA glyco-bond=------ sugar=33--33 nts=6 GGggGG H.G5,H.G4,H.BGM2,F.BGM2,F.G4,F.G5 strand#4 RNA glyco-bond=------ sugar=33--33 nts=6 GGggGG D.G5,D.G4,C.BGM2,G.BGM2,E.G4,E.G5 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4 step#1 mp(<<,backward) area=14.18 rise=3.64 twist=21.9 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2 step#2 mp(<<,backward) area=0.00 rise=6.68 twist=149.2 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2 step#3 mm(<>,outward) area=31.43 rise=3.40 twist=-15.3 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4 step#4 pm(>>,forward) area=0.00 rise=6.67 twist=-31.2 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4 6 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G5,G.G5,F.G5,E.G5 step#5 pm(>>,forward) area=13.66 rise=3.62 twist=22.6 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, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5
  step#1  pm(>>,forward)  area=14.18 rise=3.64 twist=21.9
  strand#1  U RNA glyco-bond=-- sugar=33 nts=2 GG A.G4,A.G5
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG C.G4,C.G5
  strand#3  U RNA glyco-bond=-- sugar=33 nts=2 GG H.G4,H.G5
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG D.G4,D.G5

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G4,E.G4,F.G4,G.G4
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G5,E.G5,F.G5,G.G5
  step#1  pm(>>,forward)  area=13.66 rise=3.62 twist=22.6
  strand#1  U RNA glyco-bond=-- sugar=33 nts=2 GG B.G4,B.G5
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G4,E.G5
  strand#3  U RNA glyco-bond=-- sugar=33 nts=2 GG F.G4,F.G5
  strand#4  U RNA glyco-bond=-- sugar=33 nts=2 GG G.G4,G.G5