BMRB Entry 34565

Name: NMR structure of a DNA G-quadruplex containing two SP1 binding sites from HIV-1 promoter
Published: 2022-05-26

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PDB ID: 7alu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34565
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	108
1H chemical shifts	208

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	2

Entities:

Entity 1, unit_1 22 residues - 6970.461 Da.

1

DA

DG

DA

DG

DT

DG

DT

2

DG

DC

DT

DG

DC

DG

3

DG

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_2	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	anisotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	anisotropic	sample_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