6WCK image
Deposition Date 2020-03-30
Release Date 2020-04-15
Last Version Date 2023-10-18
Entry Detail
PDB ID:
6WCK
Keywords:
Title:
KRAS G-quadruplex G16T mutant with Bromo Uracil replacing T8 and T16.
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*(BRU)P*GP*TP*GP*GP*GP*AP*AP*(BRU)P*AP*GP*GP*GP*AP*A)-3')
Mutations:T8BrU, G16BrU
Chain IDs:A, B
Chain Length:22
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A pi-stacking interactions for small-molecule recognition.
Nucleic Acids Res. 48 5766 5776 (2020)
PMID: 32313953 DOI: 10.1093/nar/gkaa262

Abstact

Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 Å) of a KRAS G-quadruplex as a 5'-head-to-head dimer with extensive poly-A π-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A π-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indicated the poly-A loop was a binding site for these ligands in addition to the 5'-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of specific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.

Legend

Protein

Chemical

Disease

Primary Citation of related structures