6SUU

NMR structure of KRAS32R G9T conformer G-quadruplex within KRAS promoter region

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

  • Deposited: 2019-09-16 Released: 2020-02-05 
  • Deposition Author(s): Marquevielle, J., Salgado, G.
  • Funding Organization(s): French League Against Cancer

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 750 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of two G-quadruplexes in equilibrium in the KRAS promoter.

Marquevielle, J.Robert, C.Lagrabette, O.Wahid, M.Bourdoncle, A.Xodo, L.E.Mergny, J.L.Salgado, G.F.

(2020) Nucleic Acids Res 48: 9336-9345

  • DOI: https://doi.org/10.1093/nar/gkaa387
  • Primary Citation of Related Structures:  
    6SUU, 6T2G

  • PubMed Abstract: 

    KRAS is one of the most mutated oncogenes and still considered an undruggable target. An alternative strategy would consist in targeting its gene rather than the protein, specifically the formation of G-quadruplexes (G4) in its promoter. G4 are secondary structures implicated in biological processes, which can be formed among G-rich DNA (or RNA) sequences. Here we have studied the major conformations of the commonly known KRAS 32R, or simply 32R, a 32 residue sequence within the KRAS Nuclease Hypersensitive Element (NHE) region. We have determined the structure of the two major stable conformers that 32R can adopt and which display slow equilibrium (>ms) with each other. By using different biophysical methods, we found that the nucleotides G9, G25, G28 and G32 are particularly implicated in the exchange between these two conformations. We also showed that a triad at the 3' end further stabilizes one of the G4 conformations, while the second conformer remains more flexible and less stable.


  • Organizational Affiliation

    European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
KRAS32R G9T32Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 750 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French League Against CancerFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-06-14
    Changes: Database references, Other
  • Version 1.4: 2024-06-19
    Changes: Data collection, Database references