BMRB Entry 34714

Name: Phen-DC3 intercalation causes hybrid-to-antiparallel transformation of human telomeric DNA G-quadruplex
Published: 2022-08-26

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PDB ID: 7z9l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34714
MolProbity Validation Chart

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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:

Phen-DC3 intercalation causes hybrid-to-antiparallel transformation of human telomeric DNA G-quadruplex

Deposition date:

2022-03-21

Original release date:

2022-08-26

Authors:

Ghosh, A.; Trajkovski, M.; Teulade-Fichou, M.; Gabelica, V.; Plavec, J.

Citation:

Citation: Ghosh, A.; Trajkovski, M.; Teulade-Fichou, M.; Gabelica, V.; Plavec, J.. "Phen-DC3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation" Angew. Chem. Int. Ed. Engl. 61, e202207384-e202207384 (2022).
PubMed: 35993443

Assembly members:

Assembly members:
entity_1, polymer, 23 residues, 7287.690 Da.
entity_PQ3, non-polymer, 550.609 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):
entity_1: TAGGGTTAGGGTTAGGGTTA GGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	231

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 23 residues - 7287.690 Da.

1

DT

DA

DG

DT

DA

DG

2

DG

DT

DA

DG

DT

DA

3

DG

Entity 2, unit_2 - C34 H26 N6 O2 - 550.609 Da.

1

PQ3

Samples:

sample_1: 23TAG, 13C at guanine, 200 uM; KCl 70 mM; potassium phosphate 20 mM

sample_2: 23TAG, 15N at guanine, 200 uM; KCl 70 mM; potassium phosphate 20 mM

sample_3: 23TAG 500 uM; KCl 70 mM; potassium phosphate 20 mM

sample_conditions_1: ionic strength: 70 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1

Software:

Amber v20, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

NMRFAM-SPARKY v1.414, Lee, Woonghee, Marco Tonelli, and John L. Markley - chemical shift assignment

TopSpin v4.1.3, Bruker Biospin - collection, processing

NMR spectrometers:

Bruker AVANCE NEO 700 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE NEO 600 MHz