BMRB Entry 30511

Name: Solution structure of 7SK stem-loop 1 with HIV-1 Tat RNA Binding Domain
Published: 2018-10-24

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PDB ID: 6mcf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR30511
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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 with HIV-1 Tat RNA Binding Domain

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.
entity_2, polymer, 17 residues, 2162.533 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
entity_2: GISYGRKKRRQRRRAHQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	134
15N chemical shifts	47
1H chemical shifts	336

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

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

Entity 2, entity_2 17 residues - 2162.533 Da.

1

GLY

ILE

SER

TYR

GLY

ARG

LYS

ARG

2

GLN

ARG

ALA

HIS

GLN

Samples:

sample_1: 7SK Stem-loop 1 RNA 0.5 ± 0.1 mM; HIV-1 Tat RNA Binding Domain, [U-13C; U-15N], 0.5 ± 0.1 mM; phosphates 10 mM; NaCl 70 mM

sample_2: 7SK Stem-loop 1 RNA 0.5 ± 0.1 mM; HIV-1 Tat RNA Binding Domain 0.5 ± 0.1 mM; phosphates 10 mM; NaCl 70 mM

sample_3: 7SK Stem-loop 1 RNA 0.5 ± 0.1 mM; HIV-1 Tat RNA Binding Domain, [U-13C; U-15N], 0.5 ± 0.1 mM; phosphates 10 mM; NaCl 70 mM

sample_4: 7SK Stem-loop 1 RNA, [U-13C; U-15N], 0.5 ± 0.1 mM; HIV-1 Tat RNA Binding Domain 0.5 ± 0.1 mM; phosphates 10 mM; NaCl 70 mM

sample_5: 7SK Stem-loop 1 RNA, [U-13C; U-15N], 0.5 ± 0.1 mM; HIV-1 Tat RNA Binding Domain 0.5 ± 0.1 mM; phosphates 10 mM; NaCl 70 mM

sample_6: 7SK Stem-loop 1 RNA 0.5 ± 0.1 mM; HIV-1 Tat RNA Binding Domain 0.5 ± 0.1 mM; phosphates 10 mM; NaCl 70 mM

sample_conditions_1: ionic strength: 80 mM; pH: 5.4; pressure: 100000 Pa; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_6	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	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

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks