BMRB Entry 30907
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PDB ID:
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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Title: Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter PubMed: 34586799
Deposition date: 2021-05-12 Original release date: 2021-10-13
Authors: Wang, K.; Dickerhoff, J.; Yang, D.
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).
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: 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: AAGGGAGGGCGGCGGGACA
- assigned_chemical_shifts
Data type | Count |
1H chemical shifts | 194 |
Additional metadata:
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 | DA | DG | DG | DG | DA | DG | DG | DG | DC | ||||
2 | DG | DG | DC | DG | DG | 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