DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 9i1p
Class: hydrolase
Method: X-ray (3.2 Å)
Summary: Structure of recql- myc g-quadruplex - adp complex from bos taurus
Reference: Song ZY, Zhang X, Ai X, Huang LY, Hou XM, Fosse P, Liu NN, Mauffret O, Rety S, Xi XG (2025): "Structural mechanism of RECQ1 helicase in unfolding G-quadruplexes compared with duplex DNA." Nucleic Acids Res., 53. doi: 10.1093/nar/gkaf877.
Abstract: RECQ1, the most abundant RecQ helicase in human cells, is involved in telomere maintenance in ALT cells and plays a critical role in maintaining genomic integrity and stability. Here, we present five high-resolution crystal structures that systematically reveal a novel mechanism by which the RECQ1 helicase recognizes and regulates G-quadruplex (G4) DNA structures. Our results demonstrate that DNA binding induces intra-subunit rearrangement in RECQ1, transitioning it from a closed to an open conformation. This rearrangement alters the stability of the dimer interface. G4 recognition and unwinding are driven by coordinated interactions between the D1/D2 domains and the single-stranded DNA (ssDNA)-binding channel. This dual engagement aligns the G4 tetrad in a geometry favorable for unwinding. ATP hydrolysis facilitates ssDNA translocation, positioning the β-hairpin to disrupt hydrogen bonds-unraveling G4 structures in a manner analogous to the unwinding of dsDNA. This study proposes a mechanistic model for RECQ1-mediated G4 unwinding and elucidates how RECQ1 recognizes and unwinds distinct DNA structures.
G4 notes: 6 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0, 3(-P-P-P)

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

List of 6 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.109 type=planar O+ nts=4 GGGG 1:E.DG2,1:E.DG6,1:E.DG11,1:E.DG15
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.092 type=planar O+ nts=4 GGGG 1:E.DG3,1:E.DG7,1:E.DG12,1:E.DG16
 3 glyco-bond=---- sugar=.-.- groove=---- planarity=0.311 type=other  O+ nts=4 GGGG 1:E.DG4,1:E.DG8,1:E.DG13,1:E.DG17
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.087 type=planar O+ nts=4 GGGG 1:F.DG2,1:F.DG6,1:F.DG11,1:F.DG15
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.084 type=planar O+ nts=4 GGGG 1:F.DG3,1:F.DG7,1:F.DG12,1:F.DG16
 6 glyco-bond=---- sugar=.-.- groove=---- planarity=0.340 type=other  O+ nts=4 GGGG 1:F.DG4,1:F.DG8,1:F.DG13,1:F.DG17

List of 2 G4-helices

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, 3 G-tetrads, INTRA-molecular, with 1 stem

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG2,1:E.DG6,1:E.DG11,1:E.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG3,1:E.DG7,1:E.DG12,1:E.DG16 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG4,1:E.DG8,1:E.DG13,1:E.DG17 step#1 pm(>>,forward) area=10.58 rise=3.23 twist=32.0 step#2 pm(>>,forward) area=12.74 rise=3.46 twist=28.0 strand#1 DNA glyco-bond=--- sugar=--. nts=3 GGG 1:E.DG2,1:E.DG3,1:E.DG4 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:E.DG6,1:E.DG7,1:E.DG8 strand#3 DNA glyco-bond=--- sugar=--. nts=3 GGG 1:E.DG11,1:E.DG12,1:E.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:E.DG15,1:E.DG16,1:E.DG17 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG2,1:E.DG6,1:E.DG11,1:E.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG3,1:E.DG7,1:E.DG12,1:E.DG16 step#1 pm(>>,forward) area=10.58 rise=3.23 twist=32.0 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG3,1:E.DG7,1:E.DG12,1:E.DG16 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG4,1:E.DG8,1:E.DG13,1:E.DG17 step#2 pm(>>,forward) area=12.74 rise=3.46 twist=28.0 Download PDB file Interactive view in 3Dmol.js

Helix#2, 3 G-tetrads, INTRA-molecular, with 1 stem

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG2,1:F.DG6,1:F.DG11,1:F.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG3,1:F.DG7,1:F.DG12,1:F.DG16 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG4,1:F.DG8,1:F.DG13,1:F.DG17 step#1 pm(>>,forward) area=10.81 rise=3.21 twist=31.9 step#2 pm(>>,forward) area=12.41 rise=3.44 twist=28.5 strand#1 DNA glyco-bond=--- sugar=--. nts=3 GGG 1:F.DG2,1:F.DG3,1:F.DG4 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:F.DG6,1:F.DG7,1:F.DG8 strand#3 DNA glyco-bond=--- sugar=--. nts=3 GGG 1:F.DG11,1:F.DG12,1:F.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:F.DG15,1:F.DG16,1:F.DG17 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG2,1:F.DG6,1:F.DG11,1:F.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG3,1:F.DG7,1:F.DG12,1:F.DG16 step#1 pm(>>,forward) area=10.81 rise=3.21 twist=31.9 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG3,1:F.DG7,1:F.DG12,1:F.DG16 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG4,1:F.DG8,1:F.DG13,1:F.DG17 step#2 pm(>>,forward) area=12.41 rise=3.44 twist=28.5 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, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG2,1:E.DG6,1:E.DG11,1:E.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG3,1:E.DG7,1:E.DG12,1:E.DG16
 3  glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:E.DG4,1:E.DG8,1:E.DG13,1:E.DG17
  step#1  pm(>>,forward)  area=10.58 rise=3.23 twist=32.0
  step#2  pm(>>,forward)  area=12.74 rise=3.46 twist=28.0
  strand#1  U DNA glyco-bond=--- sugar=--. nts=3 GGG 1:E.DG2,1:E.DG3,1:E.DG4
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:E.DG6,1:E.DG7,1:E.DG8
  strand#3  U DNA glyco-bond=--- sugar=--. nts=3 GGG 1:E.DG11,1:E.DG12,1:E.DG13
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:E.DG15,1:E.DG16,1:E.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T 1:E.DT5
  loop#2 type=propeller strands=[#2,#3] nts=2 TA 1:E.DT9,1:E.DA10
  loop#3 type=propeller strands=[#3,#4] nts=1 T 1:E.DT14

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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 1:F.DG2,1:F.DG6,1:F.DG11,1:F.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG3,1:F.DG7,1:F.DG12,1:F.DG16
 3  glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:F.DG4,1:F.DG8,1:F.DG13,1:F.DG17
  step#1  pm(>>,forward)  area=10.81 rise=3.21 twist=31.9
  step#2  pm(>>,forward)  area=12.41 rise=3.44 twist=28.5
  strand#1  U DNA glyco-bond=--- sugar=--. nts=3 GGG 1:F.DG2,1:F.DG3,1:F.DG4
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:F.DG6,1:F.DG7,1:F.DG8
  strand#3  U DNA glyco-bond=--- sugar=--. nts=3 GGG 1:F.DG11,1:F.DG12,1:F.DG13
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:F.DG15,1:F.DG16,1:F.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T 1:F.DT5
  loop#2 type=propeller strands=[#2,#3] nts=2 TA 1:F.DT9,1:F.DA10
  loop#3 type=propeller strands=[#3,#4] nts=1 T 1:F.DT14