DSSR-enabled G4 identification/annotation: PDB entry 9e2y
Summary information and primary citation
- PDB-id
- 9e2y
- Class
- replication-DNA
- Method
- cryo-EM (3.2 Å)
- Summary
- cryo-EM structure of yeast cmg helicase stalled at g4-containing DNA template, state 3
- Reference
- Batra S, Allwein B, Kumar C, Devbhandari S, Bruning JG, Bahng S, Lee CM, Marians KJ, Hite RK, Remus D (2025): "G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation." Science, 387, eadt1978. doi: 10.1126/science.adt1978.
- Abstract
- DNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we characterized fork collisions with preformed G4s in the parental DNA using reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by arresting the CMG helicase. Cryo-electron microscopy structures of stalled yeast and human CMG complexes reveal that the folded G4 is lodged inside the central CMG channel, arresting translocation. The G4 stabilizes the CMG at distinct translocation intermediates, suggesting an unprecedented helical inchworm mechanism for DNA translocation. These findings illuminate the eukaryotic replication fork mechanism under normal and perturbed conditions.
- 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=333. groove=---- planarity=0.143 type=planar O+ nts=4 GGGG F.DG38,F.DG42,F.DG46,F.DG50 2 glyco-bond=---- sugar=.3-3 groove=---- planarity=0.194 type=other O+ nts=4 GGGG F.DG39,F.DG43,F.DG47,F.DG51 3 glyco-bond=---- sugar=---3 groove=---- planarity=0.186 type=other O+ nts=4 GGGG F.DG40,F.DG44,F.DG48,F.DG52
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=333. groove=---- WC-->Major O+ nts=4 GGGG F.DG38,F.DG42,F.DG46,F.DG50 2 glyco-bond=---- sugar=.3-3 groove=---- WC-->Major O+ nts=4 GGGG F.DG39,F.DG43,F.DG47,F.DG51 3 glyco-bond=---- sugar=---3 groove=---- WC-->Major O+ nts=4 GGGG F.DG40,F.DG44,F.DG48,F.DG52 step#1 pm(>>,forward) area=11.99 rise=3.46 twist=26.1 step#2 pm(>>,forward) area=13.36 rise=3.33 twist=31.2 strand#1 DNA glyco-bond=--- sugar=3.- nts=3 GGG F.DG38,F.DG39,F.DG40 strand#2 DNA glyco-bond=--- sugar=33- nts=3 GGG F.DG42,F.DG43,F.DG44 strand#3 DNA glyco-bond=--- sugar=3-- nts=3 GGG F.DG46,F.DG47,F.DG48 strand#4 DNA glyco-bond=--- sugar=.33 nts=3 GGG F.DG50,F.DG51,F.DG52 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=333. groove=---- WC-->Major O+ nts=4 GGGG F.DG38,F.DG42,F.DG46,F.DG50 |
|
2 glyco-bond=---- sugar=.3-3 groove=---- WC-->Major O+ nts=4 GGGG F.DG39,F.DG43,F.DG47,F.DG51 |
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=333. groove=---- WC-->Major O+ nts=4 GGGG F.DG38,F.DG42,F.DG46,F.DG50 2 glyco-bond=---- sugar=.3-3 groove=---- WC-->Major O+ nts=4 GGGG F.DG39,F.DG43,F.DG47,F.DG51 3 glyco-bond=---- sugar=---3 groove=---- WC-->Major O+ nts=4 GGGG F.DG40,F.DG44,F.DG48,F.DG52 step#1 pm(>>,forward) area=11.99 rise=3.46 twist=26.1 step#2 pm(>>,forward) area=13.36 rise=3.33 twist=31.2 strand#1 U DNA glyco-bond=--- sugar=3.- nts=3 GGG F.DG38,F.DG39,F.DG40 strand#2 U DNA glyco-bond=--- sugar=33- nts=3 GGG F.DG42,F.DG43,F.DG44 strand#3 U DNA glyco-bond=--- sugar=3-- nts=3 GGG F.DG46,F.DG47,F.DG48 strand#4 U DNA glyco-bond=--- sugar=.33 nts=3 GGG F.DG50,F.DG51,F.DG52 loop#1 type=propeller strands=[#1,#2] nts=1 T F.DT41 loop#2 type=propeller strands=[#2,#3] nts=1 T F.DT45 loop#3 type=propeller strands=[#3,#4] nts=1 T F.DT49 |