BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 34542

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: Bielskute, S.; Plavec, J.; Podbevsek, P.. "Antiparallel basket-type G-quadruplex DNA structure formed in human Bcl-2 promoter containing 8-oxoG"  .

Assembly members:
entity_1, polymer, 25 residues, 7977.097 Da.

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: CGGGCGCGGGAGGAAGGGXG CGGGA

Data sets:
Data typeCount
13C chemical shifts28
1H chemical shifts152

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 25 residues - 7977.097 Da.

1   DCDGDGDGDCDGDCDGDGDG
2   DADGDGDADADGDGDG8OGDG
3   DCDGDGDGDA

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_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