BMRB Entry 31253

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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/BMR31253
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Title:
Solution structure of the major PDGFRB promoter G-quadruplex with a broken-strand G21 fill-in
Deposition date:
2025-06-25
Original release date:
2026-08-21
Authors:
Han, Y.; Dickerhoff, J.; Yang, D.
Citation:

Citation: Han, Y.; Dickerhoff, J.; Yang, D.. "Structures and Dynamics of the Major G-Quadruplex in the Human PDGFRB Gene Promoter: Insights into Vacancy G-Quadruplex Formation "  .

Assembly members:

Assembly members:
entity_1, polymer, 21 residues, 6684.297 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: AAGGGAGGGCGGCGGGGCAG G

Data sets:
Data typeCount
13C chemical shifts132
1H chemical shifts189

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 21 residues - 6684.297 Da.

1   DADADGDGDGDADGDGDGDC
2   DGDGDCDGDGDGDGDCDADG
3   DG

Samples:

sample_1: DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*G)-3') 1.06 mM; potassium chloride 75 mM; potassium phosphate 25 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

CcpNmr Analysis v2.4, CCPN - chemical shift assignment, peak picking

TopSpin, Bruker Biospin - processing

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

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

  • Bruker AVANCE III 800 MHz