6T51 | pdb_00006t51

NMR structure of KRAS22RT G-quadruplex forming within KRAS promoter region at physological temperature

• PDB DOI: https://doi.org/10.2210/pdb6T51/pdb
• BMRB: 27173
• NAKB: 6T51

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


• Deposited: 2019-10-15 Released: 2019-10-30 
• Deposition Author(s): Marquevielle, J., Salgado, G.

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Experimental Data Snapshot

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

Literature

1H,13C, and15N chemical shift assignments of a G-quadruplex forming sequence within the KRAS proto-oncogene promoter region.

Marquevielle, J., Kumar, M.V.V., Mergny, J.L., Salgado, G.F.

(2018) Biomol NMR Assign 12: 123-127

• PubMed: 29189986 
• DOI: https://doi.org/10.1007/s12104-017-9793-0
• Primary Citation Related Structures: 
  6T51


• PubMed 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 ¹ H, ¹³ C and ¹⁵ N chemical shift assignments the G4 formed within KRAS22RT sequence.

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Organizational Affiliation: 
• ARNA Laboratory, European Institute of Chemistry and Biology (IECB), Université de Bordeaux, Inserm U1212 - CNRS UMR 5320, 2, rue Robert Escarpit, 33607, Pessac, France.
ARNA Laboratory, European Institute of Chemistry and Biology (IECB), Université de Bordeaux, Inserm U1212 - CNRS UMR 5320, 2, rue Robert Escarpit, 33607, Pessac, France. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 7.06 kDa 
• Atom Count: 468 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
KRAS22RT	A	22	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	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

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Marquevielle, J., Salgado, G.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Derived calculations