BMRB Entry 30512

Name: Solution structure of 7SK stem-loop 1
Published: 2018-10-24

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PDB ID: 6mci
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30512
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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:

Solution structure of 7SK stem-loop 1

Deposition date:

2018-08-31

Original release date:

2018-10-24

Authors:

Pham, V.; D'Souza, V.

Citation:

Citation: Pham, V.; Salguero, C.; Khan, S.; Meagher, J.; Brown, W.; Humbert, N.; de Rocquigny, H.; Smith, J.; D'Souza, V.. "HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry" Nat. Commun. 9, 4266-4266 (2018).
PubMed: 30323330

Assembly members:

Assembly members:
entity_1, polymer, 57 residues, 18358.910 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGAUCUGUCACCCCAUUGA UCGCCGAGAGGCUGAUCUGG XUGGXUAGGCGGGUCCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	49
15N chemical shifts	27
1H chemical shifts	207

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 57 residues - 18358.910 Da.

1

G

A

U

C

U

G

U

C

2

A

C

A

U

G

A

3

U

C

G

C

G

A

G

A

G

4

G

C

U

G

A

U

C

U

G

5

RY

U

G

RY

U

A

G

C

6

G

U

C

Samples:

sample_1: 7SK RNA 0.5 ± 0.1 mM; NaCl 10 mM; NaCl 70 mM; EDTA 0.1 mM

sample_2: 7SK RNA, [U-13C; U-15N], 0.5 ± 0.1 mM; NaCl 10 mM; NaCl 70 mM; EDTA 0.1 mM

sample_3: 7SK RNA, [U-13C; U-15N], 0.5 ± 0.1 mM; NaCl 10 mM; NaCl 70 mM; EDTA 0.1 mM

sample_4: 7SK RNA 0.5 ± 0.1 mM; NaCl 10 mM; NaCl 70 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 80 mM; pH: 5.4; pressure: 100000 Pa; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - data analysis, processing, structure calculation

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

NMR spectrometers:

Bruker DMX 700 MHz