BMRB Entry 34670

Name: NMR Structure of the U3 RNA G-quadruplex
Published: 2023-03-28

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PDB ID: 7ps8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34670
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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 the U3 RNA G-quadruplex

Deposition date:

2021-09-22

Original release date:

2023-03-28

Authors:

Marquevielle, J.; Amrane, S.

Citation:

Citation: Marquevielle, J.; Amrane, S.. "NMR Structure of the U3 RNA G-quadruplex" .

Assembly members:

Assembly members:
entity_1, polymer, 23 residues, 7585.560 Da.
entity_K, non-polymer, 39.098 Da.

Natural source:

Natural source: Common Name: HIV-1 06TG.HT008 Taxonomy ID: 587638 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: CAGGGAGGUGUGGCCUGGGC GGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	134
15N chemical shifts	12
1H chemical shifts	177

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 23 residues - 7585.560 Da.

1

C

A

G

A

G

U

G

2

U

G

C

U

G

C

3

G

Entity 2, unit_2 - K - 39.098 Da.

1

K

Samples:

sample_1: rHIVpro3, 1H, 1.5 mM

sample_conditions_1: ionic strength: 35 mM; pH: 6.9; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMBC	sample_1	isotropic	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 NEO 950 MHz
Bruker AVANCE NEO 700 MHz
Bruker AVANCE NEO 600 MHz