DSSR-enabled G4 identification/annotation: PDB entry 6t51
Summary information and primary citation
- PDB-id
- 6t51
- Class
- DNA
- Method
- NMR
- Summary
- NMR structure of kras22rt g-quadruplex forming within kras promoter region at physological temperature
- Reference
- Marquevielle J, Kumar MVV, Mergny JL, Salgado GF (2018): "1H,13C, and15N chemical shift assignments of a G-quadruplex forming sequence within the KRAS proto-oncogene promoter region." Biomol.Nmr Assign., 12, 123-127. doi: 10.1007/s12104-017-9793-0.
- Abstract
- Single stranded guanine rich DNA (or RNA) sequences adopt noncanonical secondary structures called G-quadruplexes (G4). Functionally, quadruplexes control gene transcription and regulate activities such as replication, gene recombination or alternative splicing. Hence they are potential targets for cancer, neuronal, and viral related diseases. KRAS is one of the most mutated oncogenes in the genome of cancer cells and contains a nuclease hypersensitive element (NHE) sequence capable of forming G-quadruplexes via its six runs of guanines. In our work, we are interested in the NMR structure of the major G4 scaffold formed in the KRAS NHE region with a mutated sequence of 22 residues. Here, we report <sub>1</sub>H, <sub>13</sub>C and <sub>15</sub>N chemical shift assignments the G4 formed within KRAS22RT sequence.
- 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=0.186 type=other O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 2 glyco-bond=---- sugar=-.-- groove=---- planarity=0.252 type=other O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 glyco-bond=---- sugar=---- groove=---- planarity=0.163 type=other O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
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 A.DG2,A.DG6,A.DG11,A.DG18 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20 step#1 pm(>>,forward) area=9.70 rise=3.31 twist=29.8 step#2 pm(>>,forward) area=12.81 rise=3.30 twist=29.8 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG6,A.DG7,A.DG9 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 |
|
2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 |
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 A.DG2,A.DG6,A.DG11,A.DG18 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20 step#1 pm(>>,forward) area=9.70 rise=3.31 twist=29.8 step#2 pm(>>,forward) area=12.81 rise=3.30 twist=29.8 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2* U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG6,A.DG7,A.DG9 bulged-nts=1 T A.DT8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20 loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC5 loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT10 loop#3 type=propeller strands=[#3,#4] nts=4 AATA A.DA14,A.DA15,A.DT16,A.DA17 |