BMRB Entry 34297

Name: Adenine-driven structural switch from two- to three-quartet DNA G-quadruplex
Published: 2018-09-21

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PDB ID: 6gzn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34297
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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:

Adenine-driven structural switch from two- to three-quartet DNA G-quadruplex

Deposition date:

2018-07-04

Original release date:

2018-09-21

Authors:

Lenarcic Zivkovic, M.; Rozman, J.; Plavec, J.

Citation:

Citation: Lenarcic Zivkovic, M.; Rozman, J.; Plavec, J.. "Adenine-driven structural switch from two- to three-quartet DNA G-quadruplex." Angew. Chem. Int. Ed. Engl. 57, 15395-15399 (2018).
PubMed: 30222243

Assembly members:

Assembly members:
entity_1, polymer, 20 residues, 6410.127 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: GGGTAGGGAGCGGGAGAGGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	156

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 20 residues - 6410.127 Da.

1		DG	DG	DG	DT	DA	DG	DG	DG	DA	DG
2		DC	DG	DG	DG	DA	DG	DA	DG	DG	DG

Samples:

sample_1: DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3') 0.6 mM

sample_2: DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3') 0.8 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMR spectrometers:

Agilent DD2 600 MHz
Varian INOVA 800 MHz