DSSR-enabled G4 identification/annotation: PDB entry 9ej9
Summary information and primary citation
- PDB-id
- 9ej9
- Class
- isomerase-DNA
- Method
- cryo-EM (2.8 Å)
- Summary
- Human fancj helicase bound to a parallel g4 DNA
- Reference
- You Q, Kakusho N, Sasanuma H, Masai H, Li H (2026): "Cryo-EM structures of human FANCJ reveal the mechanism of G-quadruplex unwinding and disease-associated mutations." Nat Commun. doi: 10.1038/s41467-026-75715-0.
- Abstract
- Guanine-rich nucleic acid sequences can fold into G-quadruplex (G4) structures that regulate DNA replication, transcription, and translation. Fanconi anemia group J helicase (FANCJ) resolves G4 structures at stalled replication forks. Despite its central role in genome maintenance, the molecular basis of G4 recognition and unwinding by FANCJ has remained unclear. Here, we report cryo-EM structures of human FANCJ bound to a G4-containing DNA substrate and ATPγS. The structures reveal direct engagement of the G4 by the Fe-S domain. Structure-guided mutagenesis demonstrates that this interface is essential for G4 binding and unwinding. The structures further capture open and closed conformational states linked to ATP hydrolysis, providing a mechanism for directional translocation along 5' ssDNA and progressive G4 unwinding. Together, these findings establish the structural basis of G4 recognition by FANCJ and provide mechanistic insights into how disease-associated mutations linked to Fanconi anemia and breast cancer impair helicase function.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 2 G-tetrads
1 glyco-bond=---- sugar=3.-- groove=---- planarity=0.246 type=other O+ nts=4 GGGG B.DG17,B.DG21,B.DG26,B.DG30 2 glyco-bond=---- sugar=---3 groove=---- planarity=0.282 type=other O+ nts=4 GGGG B.DG18,B.DG22,B.DG27,B.DG31
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, 2 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=3.-- groove=---- WC-->Major O+ nts=4 GGGG B.DG17,B.DG21,B.DG26,B.DG30 2 glyco-bond=---- sugar=---3 groove=---- WC-->Major O+ nts=4 GGGG B.DG18,B.DG22,B.DG27,B.DG31 step#1 pm(>>,forward) area=15.89 rise=3.33 twist=30.9 strand#1 DNA glyco-bond=-- sugar=3- nts=2 GG B.DG17,B.DG18 strand#2 DNA glyco-bond=-- sugar=.- nts=2 GG B.DG21,B.DG22 strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG B.DG26,B.DG27 strand#4 DNA glyco-bond=-- sugar=-3 nts=2 GG B.DG30,B.DG31 |
| 1 stacking diagram | |
|
1 glyco-bond=---- sugar=3.-- groove=---- WC-->Major O+ nts=4 GGGG B.DG17,B.DG21,B.DG26,B.DG30 |
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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=3.-- groove=---- WC-->Major O+ nts=4 GGGG B.DG17,B.DG21,B.DG26,B.DG30 2 glyco-bond=---- sugar=---3 groove=---- WC-->Major O+ nts=4 GGGG B.DG18,B.DG22,B.DG27,B.DG31 step#1 pm(>>,forward) area=15.89 rise=3.33 twist=30.9 strand#1 U DNA glyco-bond=-- sugar=3- nts=2 GG B.DG17,B.DG18 strand#2 U DNA glyco-bond=-- sugar=.- nts=2 GG B.DG21,B.DG22 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG26,B.DG27 strand#4 U DNA glyco-bond=-- sugar=-3 nts=2 GG B.DG30,B.DG31 loop#1 type=propeller strands=[#1,#2] nts=2 TG B.DT19,B.DG20 loop#2 type=propeller strands=[#2,#3] nts=3 TAG B.DT23,B.DA24,B.DG25 loop#3 type=propeller strands=[#3,#4] nts=2 TG B.DT28,B.DG29 |