BMRB Entry 19387
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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/BMR19387
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
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Citation: Chung, Wan Jun; Heddi, Brahim; Tera, Masayuki; Iida, Keisuke; Nagasawa, Kazuo; Phan, Anh Tuan. "Solution structure of an intramolecular (3 + 1) human telomeric g-quadruplex bound to a telomestatin derivative." J. Am. Chem. Soc. 135, 13495-13501 (2013).
PubMed: 23909929
Assembly members:
DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), polymer, 24 residues, 7591.945 Da.
entity_L2H, non-polymer, 686.675 Da.
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'): TTGGGTTAGGGTTAGGGTTA
GGGA
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 240 |
| 31P chemical shifts | 23 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3') | 1 |
| 2 | L2H | 2 |
Entities:
Entity 1, DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3') 24 residues - 7591.945 Da.
| 1 | DT | DT | DG | DG | DG | DT | DT | DA | DG | DG | ||||
| 2 | DG | DT | DT | DA | DG | DG | DG | DT | DT | DA | ||||
| 3 | DG | DG | DG | DA |
Entity 2, L2H - C32 H34 N10 O8 - 686.675 Da.
| 1 | L2H |
Samples:
sample_1: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')0.2 – 2 mM; L2H0.2 – 2 mM; KPi 20 mM; KCl 70 mM
sample_2: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')0.2 – 2 mM; L2H0.2 – 2 mM; KPi 20 mM; KCl 70 mM
sample_3: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), [U-99% 13C; U-99% 15N], 0.2 mM; L2H 0.2 mM; KPi 20 mM; KCl 70 mM
sample_4: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), [U-99% 13C; U-99% 15N], 0.2 mM; L2H 0.2 mM; KPi 20 mM; KCl 70 mM
sample_5: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), [U-4% 13C], 0.2 – 1 mM; L2H0.2 – 1 mM; KPi 20 mM; KCl 70 mM
sample_conditions_1: ionic strength: 90 mM; pH: 7; pressure: 1 atm; temperature: 310 K
sample_conditions_2: ionic strength: 90 mM; pH: 7; pressure: 1 atm; temperature: 298 K
sample_conditions_3: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_3 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_3 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_3 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_3 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC aromatic | sample_2 | isotropic | sample_conditions_3 |
| 2D 1H-13C HSQC aromatic | sample_5 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_3 |
| 2D 1H-13C HSQC aliphatic | sample_5 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC aliphatic | sample_4 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC aromatic | sample_4 | isotropic | sample_conditions_2 |
| 1D JRHMBC | sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-31P HSQC | sample_2 | isotropic | sample_conditions_3 |
Software:
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
SPARKY, Goddard - chemical shift assignment, data analysis, peak picking
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
TOPSPIN, Bruker Biospin - collection
NMR spectrometers:
- Bruker AMX 600 MHz
- Bruker AMX 700 MHz
- Bruker AMX 400 MHz