BMRB Entry 36160
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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/BMR36160
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Title: Solution structure for the unique dimeric 4:2 complex of a platinum(II)-based tripod bound to a hybrid-1 human telomeric G-quadruplex PubMed: 30158518
Deposition date: 2018-01-31 Original release date: 2019-06-05
Authors: Liu, W.; Zhong, Y.; Liu, L.; Zeng, W.; Wang, F.; Yang, D.; Mao, Z.
Citation: Liu, Wenting; Zhong, Yi-Fang; Liu, Liu-Yi; Shen, Chu-Tong; Zeng, Wenjuan; Wang, Fuyi; Yang, Danzhou; Mao, Zong-Wan. "Solution structures of multiple G-quadruplex complexes induced by a platinum(II)-based tripod reveal dynamic binding" Nat. Commun. 9, 3496-3496 (2018).
Assembly members:
G-quadruplex DNA (26-MER), polymer, 26 residues, 8236.324 Da.
4-[1-(2,5,8-triazonia-1$l^4-platinabicyclo[3.3.0]octan-1-yl)pyridin-1-ium-4-yl]-N,N-bis[4-[1-(2,5,8-triazonia-1$l^4-platinabicyclo[3.3.0]octan-1-yl)pyridin-1-ium-4-yl]phenyl]aniline, non-polymer, 1371.303 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):
G-quadruplex DNA (26-MER): AAAGGGTTAGGGTTAGGGTT
AGGGAA
- assigned_chemical_shifts
- spectral_peak_list
Data type | Count |
1H chemical shifts | 388 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | entity_1, 1 | 1 |
2 | entity_1, 2 | 1 |
3 | entity_9F0, 1 | 2 |
4 | entity_9F0, 2 | 2 |
5 | entity_9F0, 3 | 2 |
6 | entity_9F0, 4 | 2 |
Entities:
Entity 1, entity_1, 1 26 residues - 8236.324 Da.
1 | DA | DA | DA | DG | DG | DG | DT | DT | DA | DG | ||||
2 | DG | DG | DT | DT | DA | DG | DG | DG | DT | DT | ||||
3 | DA | DG | DG | DG | DA | DA |
Entity 2, entity_9F0, 1 - C45 H63 N13 Pt3 - 1371.303 Da.
1 | 9F0 |
Samples:
sample_1: G-quadruplex DNA (26-MER), [U-15N]-Thy, 1 mM; Pt-tripod 3 mM; potassium chloride 70 mM; potassium phosphate 25 mM; H2O 90%; D2O, [U-2H], 10%
sample_2: G-quadruplex DNA (26-MER) 1 mM; Pt-tripod 3 mM; potassium chloride 70 mM; potassium phosphate 25 mM; H2O 90%; D2O, [U-2H], 10%
sample_conditions_1: ionic strength: 95 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 95 mM; pH: 7.0; pressure: 1 atm; temperature: 288 K
sample_conditions_3: ionic strength: 95 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K
Experiments:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-1H NOESY | sample_2 | anisotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_2 | anisotropic | sample_conditions_1 |
2D 1H-1H COSY | sample_2 | anisotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_2 | anisotropic | sample_conditions_2 |
2D 1H-1H TOCSY | sample_2 | anisotropic | sample_conditions_2 |
2D 1H-1H COSY | sample_2 | anisotropic | sample_conditions_2 |
2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_3 |
Software:
DISCOVER, Accelrys Software Inc. - structure calculation
SPARKY, Goddard - chemical shift assignment, peak picking
TOPSPIN, Bruker Biospin - processing
X-PLOR, Brunger - refinement
NMR spectrometers:
- Bruker AvanceIII 600 MHz
- Bruker AvanceIII 700 MHz