BMRB Entry 31099

Name: FARFAR-NMR ensemble of HIV-1 TAR with apical loop capturing ground and excited conformational states
Published: 2023-10-07

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PDB ID: 8thv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31099
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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:

FARFAR-NMR ensemble of HIV-1 TAR with apical loop capturing ground and excited conformational states

Deposition date:

2023-07-18

Original release date:

2023-10-07

Authors:

Roy, R.; Geng, A.; Shi, H.; Merriman, D.; Dethoff, E.; Salmon, L.; Al-Hashimi, H.

Citation:

Citation: Roy, R.; Geng, A.; Shi, H.; Merriman, D.; Dethoff, E.; Salmon, L.; Al-Hashimi, H.. "Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble" J. Am. Chem. Soc. 145, 22964-22978 (2023).
PubMed: 37831584

Assembly members:

Assembly members:
entity_1, polymer, 29 residues, 9307.555 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: GGCAGAUCUGAGCCUGGGAG CUCUCUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	191
15N chemical shifts	59
1H chemical shifts	224
31P chemical shifts	29

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 29 residues - 9307.555 Da.

1

G

C

A

G

A

U

C

U

G

2

A

G

C

U

G

A

G

3

C

U

C

U

C

U

G

C

Samples:

sample_1: E0_wt_TAR RNA (29-MER), [U-13C; U-15N], 1.0 mM; D2O 10%; sodium phosphate 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_2: EI22_wt_TAR RNA (29-MER), [U-13C; U-15N], 1.0 mM; D2O 10%; sodium phosphate 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_3: EII3_wt_TAR RNA (29-MER), [U-13C; U-15N], 1.0 mM; D2O 10%; sodium phosphate 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_4: EII13_wt_TAR RNA (29-MER), [U-13C; U-15N], 1.0 mM; D2O 10%; sodium phosphate 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 25 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 13C-1H S3CT HSQC	sample_1	isotropic	sample_conditions_1
2D 13C-1H S3CT HSQC	sample_1	anisotropic	sample_conditions_1
2D 13C-1H S3CT HSQC	sample_2	isotropic	sample_conditions_1
2D 13C-1H S3CT HSQC	sample_2	anisotropic	sample_conditions_1
2D 13C-1H S3CT HSQC	sample_3	isotropic	sample_conditions_1
2D 13C-1H S3CT HSQC	sample_3	anisotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_4	anisotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_4	isotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_3	anisotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_3	isotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_2	anisotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_2	isotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_1	anisotropic	sample_conditions_1
2D 13C-1H TROSY HSQC	sample_1	isotropic	sample_conditions_1
2D 13C-1H S3CT HSQC	sample_4	anisotropic	sample_conditions_1
2D 13C-1H S3CT HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Rosetta, Shi et al - structure calculation

NMR spectrometers:

Bruker AVANCE 600 MHz
Agilent Varian 800 MHz
Agilent Varian 600 MHz