7X8N

NMR Solution Structure of the Wild-type Bulge-containing KRAS-G4

PDB DOI: https://doi.org/10.2210/pdb7X8N/pdb
NAKB: 7X8N

Classification: DNA
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2022-03-14 Released: 2022-09-07
Deposition Author(s): Wang, K.B., Liu, Y., Li, J., Xiao, C., Gu, W., Li, Y., Xia, Y.Z., Yan, T., Yang, M.H., Kong, L.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insight into the bulge-containing KRAS oncogene promoter G-quadruplex bound to berberine and coptisine.

Wang, K.B., Liu, Y., Li, J., Xiao, C., Wang, Y., Gu, W., Li, Y., Xia, Y.Z., Yan, T., Yang, M.H., Kong, L.Y.

(2022) Nat Commun 13: 6016-6016

PubMed: 36224201 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-33761-4
Primary Citation of Related Structures:
7X8M, 7X8N, 7X8O

PubMed Abstract:
KRAS is one of the most highly mutated oncoproteins, which is overexpressed in various human cancers and implicated in poor survival. The G-quadruplex formed in KRAS oncogene promoter (KRAS-G4) is a transcriptional modulator and amenable to small molecule targeting. However, no available KRAS-G4-ligand complex structure has yet been determined, which seriously hinders the structure-based rational design of KRAS-G4 targeting drugs. In this study, we report the NMR solution structures of a bulge-containing KRAS-G4 bound to berberine and coptisine, respectively. The determined complex structure shows a 2:1 binding stoichiometry with each compound recruiting the adjacent flacking adenine residue to form a "quasi-triad plane" that stacks over the two external G-tetrads. The binding involves both π-stacking and electrostatic interactions. Moreover, berberine and coptisine significantly lowered the KRAS mRNA levels in cancer cells. Our study thus provides molecular details of ligand interactions with KRAS-G4 and is beneficial for the design of specific KRAS-G4-interactive drugs.

Organizational Affiliation

Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China. kbwang@cpu.edu.cn.