BMRB Entry 34881

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34881
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
A quadruplex-duplex hybrid with a three-layered chair G-quadruplex topology
Deposition date:
2023-11-22
Original release date:
2024-03-07
Authors:
Vianney, Y.; Weisz, K.
Citation:

Citation: Vianney, Y.; Dierks, D.; Weisz, K.. "Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions"  Adv. Sci. (Weinh) ., e2309891-e2309891 (2024).
PubMed: 38477454

Assembly members:

Assembly members:
entity_1, polymer, 33 residues, 10468.545 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGCGCGAAGCATTCGCGGG GTTAGGGTTXGXG

Data sets:
Data typeCount
13C chemical shifts36
1H chemical shifts219

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 33 residues - 10468.545 Da.

1   DGDGDGDCDGDCDGDADADG
2   DCDADTDTDCDGDCDGDGDG
3   DGDTDTDADGDGDGDTDTA1H3G
4   DGBGMDG

Samples:

sample_1: DNA (33-MER) 0.3 mM; potassium phosphate buffer 20 mM; KCl 100 mM

sample_2: DNA (33-MER) 0.52 mM; potassium phosphate buffer 20 mM; KCl 100 mM

sample_3: DNA (33-MER) 0.5 mM; potassium phosphate buffer 20 mM; KCl 100 mM

sample_4: DNA (33-MER), [U-10% 15N]Gua, 0.22 mM; potassium phosphate buffer 20 mM; KCl 100 mM

sample_5: DNA (33-MER), [U-10% 13C; U-10% 15N]-Gua, 0.22 mM; potassium phosphate buffer 20 mM; KCl 100 mM

sample_6: DNA (33-MER), [U-10% 15N]Ade, 0.6 mM; potassium phosphate buffer 20 mM; KCl 100 mM

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D 1H-15N HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-15N HSQCsample_6isotropicsample_conditions_2
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D DQF-COSYsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1

Software:

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

Amber v18, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

TopSpin v4.0.7, Bruker Biospin - processing

NMR spectrometers:

  • Bruker AVANCE NEO 600 MHz