BMRB Entry 30012

Title:
NMR structure of a new G-quadruplex forming sequence within the KRAS proto-oncogene promoter region
Deposition date:
2016-02-09
Original release date:
2016-03-14
Authors:
Salgado, G.; Kerkour, A.; Mergny, J.-L.
Citation:

Citation: Kerkour, Abdelaziz; Marquevielle, Julien; Ivashchenko, Stefaniia; Yatsunyk, Liliya; Mergny, Jean-Louis; Salgado, Gilmar. "High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation"  J. Biol. Chem. 292, 8082-8091 (2017).
PubMed: 28330874

Assembly members:

Assembly members:
DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*TP*GP*TP*GP*GP*GP*AP*AP*TP*AP*GP*GP*GP*AP*A)-3'), polymer, 22 residues, 6986.514 Da.
POTASSIUM ION, non-polymer, 39.098 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: homo not available

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*TP*GP*TP*GP*GP*GP*AP*AP*TP*AP*GP*GP*GP*AP*A)-3'): AGGGCGGTGTGGGAATAGGG AA

Data sets:
Data typeCount
1H chemical shifts218

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2potassium ion2

Entities:

Entity 1, entity_1 22 residues - 6986.514 Da.

1   DADGDGDGDCDGDGDTDGDT
2   DGDGDGDADADTDADGDGDG
3   DADA

Entity 2, potassium ion - 39.098 Da.

1   K

Samples:

sample_1: KRAS 22RT 2 mM; KRAS 22RT 15N, dG (5% 15N), 2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 90 mM; pH: 6.6; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HMBCsample_1isotropicsample_conditions_1
1D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

CcpNMR, CCPN - data analysis

SPARKY, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AvanceIII 700 MHz
  • Bruker AvanceIII 800 MHz