DSSR-enabled G4 identification/annotation: PDB entry 8ht7
Summary information and primary citation
- PDB-id
- 8ht7
- Class
- DNA binding protein
- Method
- NMR
- Summary
- The n-terminal region of cdc6 specifically recognizes human DNA g-quadruplex
- Reference
- Geng Y, Liu C, Xu N, Shi X, Suen MC, Zhou B, Yan B, Wu C, Li H, Song Y, Chen X, Wang Z, Cai Q, Zhu G (2024): "The N-terminal region of Cdc6 specifically recognizes human DNA G-quadruplex." Int.J.Biol.Macromol., 260, 129487. doi: 10.1016/j.ijbiomac.2024.129487.
- Abstract
- Guanine (G)-rich nucleic acid sequences can form diverse G-quadruplex structures located in functionally significant genome regions, exerting regulatory control over essential biological processes, including DNA replication in vivo. During the initiation of DNA replication, Cdc6 is recruited by the origin recognition complex (ORC) to target specific chromosomal DNA sequences. This study reveals that human Cdc6 interacts with G-quadruplex structure through a distinct region within the N-terminal intrinsically disordered region (IDR), encompassing residues 7-20. The binding region assumes a hook-type conformation, as elucidated by the NMR solution structure in complex with htel21T<sub>18</sub>. Significantly, mutagenesis and in vivo investigations confirm the highly specific nature of Cdc6's recognition of G-quadruplex. This research enhances our understanding of the fundamental mechanism governing the interaction between G-quadruplex and the N-terminal IDR region of Cdc6, shedding light on the intricate regulation of DNA replication processes.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UDUD, anti-parallel:chair, 2+2, 3(+Ln+Lw+Ln)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.077 type=planar O+ nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9 2 glyco-bond=-s-s sugar=3--3 groove=wnwn planarity=0.041 type=planar O- nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8 3 glyco-bond=-s-s sugar=3.-3 groove=wnwn planarity=0.218 type=bowl-2 O- nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
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
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1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9 2 glyco-bond=-s-s sugar=3--3 groove=wnwn WC-->Major O- nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8 3 glyco-bond=-s-s sugar=3.-3 groove=wnwn WC-->Major O- nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7 step#1 mm(<>,outward) area=9.53 rise=3.26 twist=23.2 step#2 pm(>>,forward) area=16.65 rise=3.76 twist=22.4 strand#1 DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 DNA glyco-bond=-ss sugar=--. nts=3 GGG A.DG21,A.DG20,A.DG19 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 DNA glyco-bond=-ss sugar=-33 nts=3 GGG A.DG9,A.DG8,A.DG7 |
| 2 stacking diagrams | |
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1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9 |
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2 glyco-bond=-s-s sugar=3--3 groove=wnwn WC-->Major O- nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8 |
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, UDUD, anti-parallel:chair, 2+2, 3(+Ln+Lw+Ln)
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1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9 2 glyco-bond=-s-s sugar=3--3 groove=wnwn WC-->Major O- nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8 3 glyco-bond=-s-s sugar=3.-3 groove=wnwn WC-->Major O- nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7 step#1 mm(<>,outward) area=9.53 rise=3.26 twist=23.2 step#2 pm(>>,forward) area=16.65 rise=3.76 twist=22.4 strand#1 U DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 D DNA glyco-bond=-ss sugar=--. nts=3 GGG A.DG21,A.DG20,A.DG19 strand#3 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 D DNA glyco-bond=-ss sugar=-33 nts=3 GGG A.DG9,A.DG8,A.DG7 loop#1 type=lateral strands=[#1,#4] nts=3 TTA A.DT4,A.DT5,A.DA6 loop#2 type=lateral strands=[#4,#3] nts=3 TTA A.DT10,A.DT11,A.DA12 loop#3 type=lateral strands=[#3,#2] nts=3 TTT A.DT16,A.DT17,A.DT18 |