BMRB Entry 25686
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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/BMR25686
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Title: Structure of a G-quadruplex in the Long Terminal Repeat of the proviral HIV-1 genome PubMed: 27298260
Deposition date: 2015-07-02 Original release date: 2016-06-27
Authors: De Nicola, Beatrice; Lech, Christopher Jacques; Regmi, Sagar; Heddi, Brahim; Richter, Sara; Phan, Anh Tuan
Citation: de Nicola, Beatrice; Lech, Christopher Jacques; Regmi, Sagar; Heddi, Brahim; Richter, Sara; Phan, Anh Tuan. "Structure of a G-quadruplex in the Long Terminal Repeat of the proviral HIV-1 genome" Nucleic Acids Res. 44, 6442-6451 (2016).
Assembly members:
DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3'), polymer, 22 residues, 6945.505 Da.
Natural source: Common Name: viruses Taxonomy ID: 12721 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3'): CTGGGCGGGACTGGGGAGTG
GT
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 209 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') | 1 |
Entities:
Entity 1, DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') 22 residues - 6945.505 Da.
| 1 | DC | DT | DG | DG | DG | DC | DG | DG | DG | DA | ||||
| 2 | DC | DT | DG | DG | DG | DG | DA | DG | DT | DG | ||||
| 3 | DG | DT |
Samples:
sample_1: DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')0.1 – 1 mM; K+ 10 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 90 mM; pH: 7.0; 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 TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 1D JR-HMQC | sample_1 | isotropic | sample_conditions_1 |
Software:
SPARKY, Goddard - chemical shift assignment, data analysis, peak picking
TOPSPIN, Bruker Biospin - collection
X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, structure solution
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 700 MHz