BMRB Entry 34565

Title:
NMR structure of a DNA G-quadruplex containing two SP1 binding sites from HIV-1 promoter
Deposition date:
2020-10-07
Original release date:
2022-05-26
Authors:
Marquevielle, J.; Amrane, S.
Citation:

Citation: De Rache, A.; Marquevielle, J.; Bouaziz, S.; Vialet, B.; Andreola, M.; Mergny, J.; Amrane, S.. "Structure of a DNA G-quadruplex that Modulates SP1 Binding Sites Architecture in HIV-1 Promoter"  J. Mol. Biol. 436, 168359-168359 (2024).
PubMed: 37952768

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 6970.461 Da.
entity_K, non-polymer, 39.098 Da.

Natural source:

Natural source:   Common Name: HIV-1   Taxonomy ID: 11676   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus HIV-1

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AGGGAGGTGTGGCCTGGGCG GG

Data sets:
Data typeCount
13C chemical shifts108
1H chemical shifts208

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_32

Entities:

Entity 1, unit_1 22 residues - 6970.461 Da.

1   DADGDGDGDADGDGDTDGDT
2   DGDGDCDCDTDGDGDGDCDG
3   DGDG

Entity 2, unit_2 - K - 39.098 Da.

1   K

Samples:

sample_1: HIVpro2 2.4 mM; KCl 70 mM; KPi 20 mM

sample_2: HIVpro2 857 uM; KCl 70 mM; KPi 20 mM

sample_conditions_1: ionic strength: 90 mM; pH: 6.9; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2anisotropicsample_conditions_1
2D 1H-1H NOESYsample_1anisotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1anisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1anisotropicsample_conditions_1
2D 1H-1H TOCSYsample_1anisotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - data analysis

Sparky, Goddard - chemical shift assignment

ARIA, Linge, O'Donoghue and Nilges - structure calculation

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

NMR spectrometers:

  • Bruker AVANCE III 400 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE III 800 MHz