BMRB Entry 30788

Name: The FARFAR-NMR Ensemble of 29-mer HIV-1 Trans-activation Response Element RNA (N=20)
Published: 2020-10-05

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PDB ID: 7ju1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30788
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

The FARFAR-NMR Ensemble of 29-mer HIV-1 Trans-activation Response Element RNA (N=20)

Deposition date:

2020-08-18

Original release date:

2020-10-05

Authors:

Shi, H.; Rangadurai, A.; Roy, R.; Yesselman, J.; Al-Hashimi, H.

Citation:

Citation: Shi, H.; Rangadurai, A.; Abou-Assi, H.; Roy, R.; Case, D.; Herschlag, D.; Yesselman, J.; Al-Hashimi, H.. "Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction" Nat. Commun. 11, 5531-5531 (2020).
PubMed: 33139729

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	8
1H chemical shifts	222

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: mtTAR_E0, [U-13C; U-15N], 1.0 mM

sample_2: mtTAR_EI22, [U-13C; U-15N], 1.0 mM

sample_3: mtTAR_EII22, [U-13C; U-15N], 1.0 mM

sample_4: mtTAR_EI3, [U-13C; U-15N], 1.0 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 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C TROSY	sample_1	anisotropic	sample_conditions_1
2D 1H-13C TROSY	sample_4	anisotropic	sample_conditions_1
2D 1H-13C TROSY	sample_3	anisotropic	sample_conditions_1
2D 1H-13C TROSY	sample_2	anisotropic	sample_conditions_1
2D 1H-13C S3CT HSQC	sample_4	anisotropic	sample_conditions_1
2D 1H-13C S3CT HSQC	sample_3	anisotropic	sample_conditions_1
2D 1H-13C S3CT HSQC	sample_2	anisotropic	sample_conditions_1
2D 1H-13C S3CT HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC without decoupling	sample_4	anisotropic	sample_conditions_1
2D 1H-15N HSQC without decoupling	sample_3	anisotropic	sample_conditions_1
2D 1H-15N HSQC without decoupling	sample_2	anisotropic	sample_conditions_1
2D 1H-15N HSQC without decoupling	sample_1	anisotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

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

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 600 MHz