BMRB Entry 36160

Name: Solution structure for the unique dimeric 4:2 complex of a platinum(II)-based tripod bound to a hybrid-1 human telomeric G-quadruplex
Published: 2019-06-05

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PDB ID: 5z8f
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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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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

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:

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).
PubMed: 30158518

Assembly members:

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:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
G-quadruplex DNA (26-MER): AAAGGGTTAGGGTTAGGGTT AGGGAA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
1H chemical shifts	388

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

DG

DT

DA

DG

2

DG

DT

DA

DG

DT

3

DA

DG

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