DSSR-enabled G4 identification/annotation: PDB entry 9i22
Summary information and primary citation
- PDB-id
- 9i22
- Class
- hydrolase
- Method
- X-ray (2.42 Å)
- Summary
- Structure of human helicase recq1- myc g-quadruplex - adp complex
- 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
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.061 type=planar O+ nts=4 GGGG 1:C.DG2,1:C.DG6,1:C.DG11,1:C.DG15 2 glyco-bond=---- sugar=---- groove=---- planarity=0.058 type=planar O+ nts=4 GGGG 1:C.DG3,1:C.DG7,1:C.DG12,1:C.DG16 3 glyco-bond=---- sugar=.-.- groove=---- planarity=0.290 type=other O+ nts=4 GGGG 1:C.DG4,1:C.DG8,1:C.DG13,1:C.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, 3 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:C.DG2,1:C.DG6,1:C.DG11,1:C.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:C.DG3,1:C.DG7,1:C.DG12,1:C.DG16 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:C.DG4,1:C.DG8,1:C.DG13,1:C.DG17 step#1 pm(>>,forward) area=11.79 rise=3.31 twist=31.2 step#2 pm(>>,forward) area=12.51 rise=3.44 twist=28.5 strand#1 DNA glyco-bond=--- sugar=--. nts=3 GGG 1:C.DG2,1:C.DG3,1:C.DG4 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:C.DG6,1:C.DG7,1:C.DG8 strand#3 DNA glyco-bond=--- sugar=--. nts=3 GGG 1:C.DG11,1:C.DG12,1:C.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:C.DG15,1:C.DG16,1:C.DG17 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:C.DG2,1:C.DG6,1:C.DG11,1:C.DG15 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:C.DG3,1:C.DG7,1:C.DG12,1:C.DG16 |
List of 1 G4-stem
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:C.DG2,1:C.DG6,1:C.DG11,1:C.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:C.DG3,1:C.DG7,1:C.DG12,1:C.DG16 3 glyco-bond=---- sugar=.-.- groove=---- WC-->Major O+ nts=4 GGGG 1:C.DG4,1:C.DG8,1:C.DG13,1:C.DG17 step#1 pm(>>,forward) area=11.79 rise=3.31 twist=31.2 step#2 pm(>>,forward) area=12.51 rise=3.44 twist=28.5 strand#1 U DNA glyco-bond=--- sugar=--. nts=3 GGG 1:C.DG2,1:C.DG3,1:C.DG4 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:C.DG6,1:C.DG7,1:C.DG8 strand#3 U DNA glyco-bond=--- sugar=--. nts=3 GGG 1:C.DG11,1:C.DG12,1:C.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:C.DG15,1:C.DG16,1:C.DG17 loop#1 type=propeller strands=[#1,#2] nts=1 T 1:C.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TA 1:C.DT9,1:C.DA10 loop#3 type=propeller strands=[#3,#4] nts=1 T 1:C.DT14 |