BMRB Entry 34542

Name: Antiparallel basket-type G-quadruplex DNA structure formed in human Bcl-2 promoter containing 8-oxoG
Published: 2021-03-08

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PDB ID: 6zx6
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34542
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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:

Antiparallel basket-type G-quadruplex DNA structure formed in human Bcl-2 promoter containing 8-oxoG

Deposition date:

2020-07-29

Original release date:

2021-03-08

Authors:

Bielskute, S.; Plavec, J.; Podbevsek, P.

Citation:

Citation: Bielskute, S.; Plavec, J.; Podbevsek, P.. "Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter" Nucleic Acids Res. 49, 2346-2356 (2021).
PubMed: 33638996

Assembly members:

Assembly members:
entity_1, polymer, 25 residues, 7977.097 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: CGGGCGCGGGAGGAAGGGXG CGGGA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	28
1H chemical shifts	152

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 25 residues - 7977.097 Da.

1

DC

DG

DC

DG

DC

DG

2

DA

DG

DA

DG

8OG

DG

3

DC

DG

DA

Samples:

sample_1: bcl2ex-oxoG19 1.2 mM

sample_2: bcl2ex-oxoG19 1.2 mM

sample_conditions_1: ionic strength: 90 mM; pH: 7; pressure: 101325 Pa; temperature: 298 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 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1

Software:

CcpNmr Analysis, CCPN - chemical shift assignment

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

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian DD2 800 MHz
Varian DD2 600 MHz