BMRB Entry 30923

Name: Solution structure of the MYC promoter G-quadruplex in complex with berberine: conformer A
Published: 2021-10-30

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PDB ID: 7n7d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30923
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	27
1H chemical shifts	222

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	2

Entities:

Entity 1, unit_1 22 residues - 7033.523 Da.

1

DT

DG

DA

DG

DT

DG

2

DT

DA

DG

DT

DG

3

DA

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_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