Summary information

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 1H, 13C and 15N chemical shift assignments the G4 formed within KRAS22RT sequence.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.186 type=other  nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2 glyco-bond=---- sugar=..-- groove=---- planarity=0.252 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.163 type=other  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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2  glyco-bond=---- sugar=..-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major 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

Download PDB file
Interactive view in 3Dmol.js
2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2  glyco-bond=---- sugar=..-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
  step#1  pm(>>,forward)  area=9.70  rise=3.31 twist=29.8

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=..-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20
  step#2  pm(>>,forward)  area=12.81 rise=3.30 twist=29.8

Download PDB file
Interactive view in 3Dmol.js

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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18
 2  glyco-bond=---- sugar=..-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major 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

Download PDB file
Interactive view in 3Dmol.js