BMRB Entry 17697

Name: Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface
Published: 2011-08-19

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PDB ID: 2le6
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17697
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface PubMed: 21840903

Deposition date: 2011-06-10 Original release date: 2011-08-19

Authors: Do, Ngoc Quang; Lim, Kah Wai; Teo, Ming Hoon; Heddi, Brahim; Phan, Anh Tuan

Citation: Do, Ngoc Quang; Lim, Kah Wai; Teo, Ming Hoon; Heddi, Brahim; Phan, Anh Tuan. "Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity." Nucleic Acids Res. 39, 9448-9457 (2011).

Assembly members:
DNA_(5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')_, polymer, 16 residues, 5107.312 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(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')_: GXGTGGGTGGGTGGGT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	127

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	G-quadruplex_strand_1	1
2	G-quadruplex_strand_2	1

Entities:

Entity 1, G-quadruplex_strand_1 16 residues - 5107.312 Da.

1

DG

DI

DG

DT

DG

DT

DG

2

DG

DT

DG

DT

Samples:

sample_1: G-quadruplex0.5 – 2.0 mM; H2O 90%; D2O 10%

sample_2: G-quadruplex0.5 – 2.0 mM; D2O 100%

sample_3: G-quadruplex, [U-2% 15N; U-2% 13C], 0.5 – 2.0 mM; H2O 90%; D2O 10%

sample_4: G-quadruplex, [U-100% 2H], 0.5 – 2.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 90 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C JR HMBC	sample_1	isotropic	sample_conditions_1
2D 1H-1H JR NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
H-D exchange	sample_2	isotropic	sample_conditions_1
15N-filtered	sample_3	isotropic	sample_conditions_1
D-labeled	sample_4	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - processing

FELIX v2007, Felix NMR, Inc. - peak picking

X-PLOR NIH v2.27, Schwieters, Kuszewski, Tjandra and Clore - structure solution

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz