BMRB Entry 30907

Name: Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter
Published: 2021-10-13

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PDB ID: 7msv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30907
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter

Deposition date:

2021-05-12

Original release date:

2021-10-13

Authors:

Wang, K.; Dickerhoff, J.; Yang, D.

Citation:

Citation: Wang, K.; Dickerhoff, J.; Yang, D.. "Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-beta Promoter" J. Am. Chem. Soc. 143, 16549-16555 (2021).
PubMed: 34586799

Assembly members:

Assembly members:
entity_1, polymer, 19 residues, 6009.886 Da.
entity_DGP, non-polymer, 347.221 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: AAGGGAGGGCGGCGGGACA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	194

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	3
4	unit_4	3

Entities:

Entity 1, unit_1 19 residues - 6009.886 Da.

1

DA

DG

DA

DG

DC

2

DG

DC

DG

DA

DC

DA

Entity 2, unit_2 - C10 H14 N5 O7 P - 347.221 Da.

1

DGP

Entity 3, unit_3 - C20 H18 N O4 - 336.361 Da.

1

BER

Samples:

sample_1: BER-dGMP-Pu19m2 1.5 mM

sample_2: dGMP, [U-100% 13C; U-100% 15N], 9 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 760 mmHg; temperature: 298 K

sample_conditions_2: ionic strength: 50 mM; pH: 7.0; pressure: 760 mmHg; temperature: 288 K

sample_conditions_3: ionic strength: 50 mM; pH: 7.0; pressure: 760 mmHg; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_3
2D 1H-13C HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	anisotropic	sample_conditions_1
1D GEJRSE HMQC	sample_2	anisotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL. - chemical shift assignment

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

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

NMR spectrometers:

Bruker AV-500 500 MHz
Bruker AV-800 800 MHz