BMRB Entry 30923

Title:
Solution structure of the MYC promoter G-quadruplex in complex with berberine: conformer A
Deposition date:
2021-06-10
Original release date:
2021-10-30
Authors:
Dickerhoff, J.; Yang, D.
Citation:

Citation: Dickerhoff, J.; Brundridge, N.; McLuckey, S.; Yang, D.. "Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution"  J. Med. Chem. 64, 16205-16212 (2021).
PubMed: 34677968

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 7033.523 Da.
entity_BER, non-polymer, 336.361 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TGAGGGTGGGTAGGGTGGGG AA

Data sets:
Data typeCount
13C chemical shifts27
1H chemical shifts222

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_32

Entities:

Entity 1, unit_1 22 residues - 7033.523 Da.

1   DTDGDADGDGDGDTDGDGDG
2   DTDADGDGDGDTDGDGDGDG
3   DADA

Entity 2, unit_2 - C20 H18 N O4 - 336.361 Da.

1   BER

Samples:

sample_1: DNA 1.2 mM; Berberine 3.6 mM; potassium phosphate 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1

Software:

Amber v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - structure calculation

X-PLOR NIH v2.48, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

CcpNmr Analysis v2.4, CCPN - chemical shift assignment, peak picking

TopSpin, Bruker Biospin - processing

NMR spectrometers:

  • Bruker AVANCE III 800 MHz