DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 8vx1
Class: motor protein
Method: cryo-EM (3.4 Å)
Summary: cryo-EM structure of dhx36 bound to the cmyc DNA g-quadruplex, class 2
Reference: Banco MT, Paul T, Jiang J, Myong S, Ferre-D'Amare AR: "Inter-domain synergy enables both DNA and RNA G-quadruplex unwinding by the DEAH-box helicase DHX36."
Abstract
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 3(-P-P); UUUU, parallel, 4+0, 3(-P-P-P), coaxial interfaces: 5'/5'

Cartoon-block schematics in six views (download the tarball)

List of 6 G-tetrads

 1 glyco-bond=---- sugar=.--- groove=---- planarity=0.140 type=planar O+ nts=4 GGGG C.DG2,C.DG6,C.DG11,C.DG15
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.107 type=planar O+ nts=4 GGGG C.DG3,C.DG7,C.DG12,C.DG16
 3 glyco-bond=---- sugar=-3-- groove=---- planarity=0.295 type=other  O+ nts=4 GGGG C.DG4,C.DG8,C.DG13,C.DG17
 4 glyco-bond=---- sugar=---. groove=---- planarity=0.174 type=other  O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15
 5 glyco-bond=---- sugar=---3 groove=---- planarity=0.235 type=other  O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.308 type=other  O+ nts=4 GGGG B.DG4,B.DG8,B.DG13,B.DG17

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-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG C.DG4,C.DG8,C.DG13,C.DG17 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG C.DG3,C.DG7,C.DG12,C.DG16 3* glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG C.DG2,C.DG6,C.DG11,C.DG15 4 glyco-bond=---- sugar=--.- groove=---- Major-->WC O+ nts=4 GGGG B.DG6,B.DG2,B.DG15,B.DG11 5 glyco-bond=---- sugar=--3- groove=---- Major-->WC O+ nts=4 GGGG B.DG7,B.DG3,B.DG16,B.DG12 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG8,B.DG4,B.DG17,B.DG13 step#1 mp(<<,backward) area=16.80 rise=3.34 twist=25.9 step#2 mp(<<,backward) area=9.94 rise=3.28 twist=32.5 step#3 mm(<>,outward) area=26.53 rise=3.64 twist=-6.5 step#4 pm(>>,forward) area=10.28 rise=3.23 twist=34.2 step#5 pm(>>,forward) area=17.51 rise=3.38 twist=24.3 strand#1 DNA glyco-bond=------ sugar=--.--- nts=6 GGGGGG C.DG4,C.DG3,C.DG2,B.DG6,B.DG7,B.DG8 strand#2 DNA glyco-bond=------ sugar=3----- nts=6 GGGGGG C.DG8,C.DG7,C.DG6,B.DG2,B.DG3,B.DG4 strand#3 DNA glyco-bond=------ sugar=---.3- nts=6 GGGGGG C.DG13,C.DG12,C.DG11,B.DG15,B.DG16,B.DG17 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG C.DG17,C.DG16,C.DG15,B.DG11,B.DG12,B.DG13 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG C.DG4,C.DG8,C.DG13,C.DG17 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG C.DG3,C.DG7,C.DG12,C.DG16 step#1 mp(<<,backward) area=16.80 rise=3.34 twist=25.9 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG C.DG3,C.DG7,C.DG12,C.DG16 3* glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG C.DG2,C.DG6,C.DG11,C.DG15 step#2 mp(<<,backward) area=9.94 rise=3.28 twist=32.5 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG C.DG2,C.DG6,C.DG11,C.DG15 4 glyco-bond=---- sugar=--.- groove=---- Major-->WC O+ nts=4 GGGG B.DG6,B.DG2,B.DG15,B.DG11 step#3 mm(<>,outward) area=26.53 rise=3.64 twist=-6.5 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=--.- groove=---- Major-->WC O+ nts=4 GGGG B.DG6,B.DG2,B.DG15,B.DG11 5 glyco-bond=---- sugar=--3- groove=---- Major-->WC O+ nts=4 GGGG B.DG7,B.DG3,B.DG16,B.DG12 step#4 pm(>>,forward) area=10.28 rise=3.23 twist=34.2 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=--3- groove=---- Major-->WC O+ nts=4 GGGG B.DG7,B.DG3,B.DG16,B.DG12 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG8,B.DG4,B.DG17,B.DG13 step#5 pm(>>,forward) area=17.51 rise=3.38 twist=24.3 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, 3 G-tetrads, 2 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P)

 1  glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG C.DG2,C.DG6,C.DG11,C.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG C.DG3,C.DG7,C.DG12,C.DG16
 3  glyco-bond=---- sugar=-3-- groove=---- WC-->Major O+ nts=4 GGGG C.DG4,C.DG8,C.DG13,C.DG17
  step#1  pm(>>,forward)  area=9.94  rise=3.28 twist=32.5
  step#2  pm(>>,forward)  area=16.80 rise=3.34 twist=25.9
  strand#1  U DNA glyco-bond=--- sugar=.-- nts=3 GGG C.DG2,C.DG3,C.DG4
  strand#2  U DNA glyco-bond=--- sugar=--3 nts=3 GGG C.DG6,C.DG7,C.DG8
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG11,C.DG12,C.DG13
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG15,C.DG16,C.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T C.DT5
  loop#2 type=propeller strands=[#3,#4] nts=1 T C.DT14

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)

 1  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15
 2  glyco-bond=---- sugar=---3 groove=---- WC-->Major O+ nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.DG4,B.DG8,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=10.28 rise=3.23 twist=34.2
  step#2  pm(>>,forward)  area=17.51 rise=3.38 twist=24.3
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG6,B.DG7,B.DG8
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- sugar=.3- nts=3 GGG B.DG15,B.DG16,B.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT5
  loop#2 type=propeller strands=[#2,#3] nts=2 TA B.DT9,B.DA10
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT14