BMRB Entry 31106

Name: The FARFAR-MD-NMR ensemble of an HIV-1 TAR excited state
Published: 2023-10-16

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PDB ID: 8u3m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31106
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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:

The FARFAR-MD-NMR ensemble of an HIV-1 TAR excited state

Deposition date:

2023-09-07

Original release date:

2023-10-16

Authors:

Geng, A.; Ganser, L.; Roy, R.; Shi, H.; Pratihar, S.; Case, D.; Al-Hashimi, H.

Citation:

Citation: Geng, A.; Ganser, L.; Roy, R.; Shi, H.; Pratihar, S.; Case, D.; Al-Hashimi, H.. "An RNA excited conformational state at atomic resolution" Nat. Commun. 14, 8432-8432 (2023).
PubMed: 38114465

Assembly members:

Assembly members:
entity_1, polymer, 31 residues, 9918.902 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: GGCAGAUCUGAGCCUUCGGG AGCUCUCUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	87
15N chemical shifts	12
1H chemical shifts	100

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 31 residues - 9918.902 Da.

1

G

C

A

G

A

U

C

U

G

2

A

G

C

U

C

G

3

A

G

C

U

C

U

C

U

G

C

4

C

Samples:

sample_1: UUCGES2_TAR, [U-100% 13C; U-100% 15N], 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 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC sugar	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC sugar	sample_1	anisotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

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

Rosetta, Honglue Shi - structure calculation

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

NMR spectrometers:

Bruker AVANCE 600 MHz