BMRB Entry 35028

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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/BMR35028
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
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Title:
L12 G-quadruplex-forming aptamer targeting HMGB1 protein
Deposition date:
2025-12-16
Original release date:
2026-04-01
Authors:
Trajkovski, M.; Platella, C.; Napolitano, E.; Esposito, C.; Catuogno, S.; Musumeci, D.; Plavec, J.; Montesarchio, D.
Citation:

Citation: Trajkovski, Marko; Platella, Chiara; Musumeci, Domenica; Napolitano, Ettore; Esposito, Carla Lucia; Catuogno, Silvia; Plavec, Janez; Montesarchio, Daniela. "Unraveling the NMR structures of G-quadruplex-forming aptamers acting as inhibitors of High Mobility Group Box 1 (HMGB1) pathological activity"  Int. J. Biol. Macromol. 357, 151585-151585 (2026).
PubMed: 41881226

Assembly members:

Assembly members:
entity_1, polymer, 26 residues, 8209.282 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: TTAGGGATTGGGAATGGGTA TGGGTT

Data sets:
Data typeCount
1H chemical shifts243

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 26 residues - 8209.282 Da.

1   DTDTDADGDGDGDADTDTDG
2   DGDGDADADTDGDGDGDTDA
3   DTDGDGDGDTDT

Samples:

sample_1: DNA (26-MER) 1.0 mM; potassium phosphate 20 mM; KCl 100 mM

sample_2: DNA (26-MER), NA-95%,U-5% 13C, U-5% 15N, 0.2 mM; potassium phosphate 20 mM; KCl 100 mM

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 bar; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1

Software:

NMRFAM-SPARKY, Lee W., Tonelli M., Makley J.L. - chemical shift assignment

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

TopSpin, Bruker Biospin - data analysis

NMR spectrometers:

  • Bruker AVANCE NEO 600 MHz
  • Bruker AVANCE NEO 800 MHz