BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30804

Title: Solution structure of the major MYC promoter G-quadruplex with a wild-type flanking in complex with NSC85697, a quinoline derivative   PubMed: 33978746

Deposition date: 2020-10-03 Original release date: 2021-06-18

Authors: Dickerhoff, J.; Yang, D.

Citation: Dickerhoff, Jonathan; Dai, Jixun; Yang, Danzhou. "Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes"  Nucleic Acids Res. 49, 5905-5915 (2021).

Assembly members:
entity_1, polymer, 22 residues, 7033.523 Da.
entity_WAM, non-polymer, 335.376 Da.

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: TGAGGGTGGGTAGGGTGGGG AA

Data sets:
Data typeCount
13C chemical shifts26
1H chemical shifts218

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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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 H19 N2 O3 - 335.376 Da.

1   WAM

Samples:

sample_1: Myc2345 0.8 mM; NSC85697 2.4 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: 288 K

sample_conditions_3: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D NOESYsample_1isotropicsample_conditions_2
2D NOESYsample_1isotropicsample_conditions_3
2D DQF-COSYsample_1isotropicsample_conditions_3
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1

Software:

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

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

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AVANCE III 800 MHz