BMRB Entry 36746

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36746
MolProbity Validation Chart

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Title:
Structure of AA(GGGTT)3GGGAA G-quadruplex in the presence of sodium ions
Deposition date:
2025-03-25
Original release date:
2026-06-06
Authors:
Negi, D.; Sannapureddi, R.; Sathyamoorthy, B.
Citation:

Citation: Negi, D.; Sannapureddi, R.; Sathyamoorthy, B.; Reddy Sannapureddi, R.; Mohanty, M.; Gautam, A.; Sathyamoorthy, B.. "Molecular Interactions of a Frustrated G-Rich Sequence: Atomistic Insights into Folding of DNA G-Quadruplexes"  .

Assembly members:

Assembly members:
DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), polymer, 22 residues, 6983.497 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: chemical synthesis   Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'): AAGGGTTGGGTTGGGTTGGG AA

Data sets:
Data typeCount
13C chemical shifts75
15N chemical shifts12
1H chemical shifts133

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 22 residues - 6983.497 Da.

1   DADADGDGDGDTDTDGDGDG
2   DTDTDGDGDGDTDTDGDGDG
3   DADA

Samples:

sample_1: DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3') 1.5 ± 0.1 mM; sodium chloride 50 ± 0.1 mM; sodium phosphate 20 ± 0.1 mM; dss 50 ± 0.1 uM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 418 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 418 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HMQCsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC F2 coupledsample_1isotropicsample_conditions_1
2D 1H-13C HSQC F2 coupledsample_1isotropicsample_conditions_2

Software:

TopSpin, Bruker Biospin - collection

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

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization

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

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

NMR spectrometers:

  • Bruker AVANCE III 700 MHz