BMRB Entry 25746
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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/BMR25746
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Title: G-quadruplex structure PubMed: 26673723
Deposition date: 2015-08-08 Original release date: 2016-05-31
Authors: Heddi, Brahim; Martin-Pintado, Nerea; Serimbetov, Zhalgas; Kari, Teuku; Phan, Anh Tuan
Citation: Heddi, Brahim; Martin-Pintado, Nerea; Serimbetov, Zhalgas; Kari, Teuku; Phan, Anh Tuan. "G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triadwater complex and implication for small-molecule binding" Nucleic Acids Res. 44, 910-916 (2016).
Assembly members:
DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'), polymer, 18 residues, 5705.705 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):
DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'): TTGTGTGGGTGGGTGGGT
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 114 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') | 1 |
Entities:
Entity 1, DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 18 residues - 5705.705 Da.
| 1 | DT | DT | DG | DT | DG | DT | DG | DG | DG | DT | ||||
| 2 | DG | DG | DG | DT | DG | DG | DG | DT |
Samples:
sample_1: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')0.1 – 1.2 mM; H2O 90%; D2O 10%
sample_2: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'), [U-4% 15N], 0.2-0.4 mM; H2O 90%; D2O 10%
sample_3: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 0.6-1.2 mM; D2O 100%
sample_4: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'), [U-100% 2H], 0.2-0.4 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 45 mM; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H HMBC | sample_1 | isotropic | sample_conditions_1 |
| 1D 15N-filtered 1H NMR | sample_2 | isotropic | sample_conditions_1 |
| 1D 1H NMR | sample_4 | isotropic | sample_conditions_1 |
| 1D 1H NMR | sample_1 | isotropic | sample_conditions_1 |
Software:
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution
SPARKY, Goddard - chemical shift assignment, chemical shift calculation, data analysis, peak picking
TOPSPIN, Bruker Biospin - collection
X-PLOR, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement
Spinworks, http://home.cc.umanitoba.ca/~wolowiec/spinworks - data analysis
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 700 MHz