BMRB Entry 30971

Name: Solution structure of 7SK stem-loop 1 with HEXIM Arginine Rich Motif
Published: 2022-09-08

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PDB ID: 7t1n
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30971
MolProbity Validation Chart

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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 HEXIM Arginine Rich Motif

Deposition date:

2021-12-02

Original release date:

2022-09-08

Authors:

Pham, V.; Gao, M.; D'Souza, V.

Citation:

Citation: Pham, V.; Gao, M.; Meagher, J.; Smith, J.; D'Souza, V.. "A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA" Commun. Biol. 5, 819-819 (2022).
PubMed: 35970937

Assembly members:

Assembly members:
entity_1, polymer, 56 residues, 17986.635 Da.
entity_2, polymer, 19 residues, 2285.681 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 UCGCCAGUGGCUGAUCUGGC UGGCUAGGCGGGUCCC
entity_2: GISYGRQLGKKKHRRRAHQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	123
15N chemical shifts	50
1H chemical shifts	230

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 56 residues - 17986.635 Da.

1

G

A

U

C

U

G

U

C

2

A

C

A

U

G

A

3

U

C

G

C

A

G

U

G

4

C

U

G

A

U

C

U

G

C

5

U

G

C

U

A

G

C

G

6

G

U

C

Entity 2, unit_2 19 residues - 2285.681 Da.

1

GLY

ILE

SER

TYR

GLY

ARG

GLN

LEU

GLY

LYS

2

LYS

HIS

ARG

ALA

HIS

GLN

Samples:

sample_1: HEXIM 0.5 ± 0.2 mM; 7SK 0.5 ± 0.2 mM; NaCl 70 mM; EDTA 0.1 mM

sample_2: HEXIM 0.5 ± 0.2 mM; 7SK 0.5 ± 0.2 mM; NaCl 70 mM; EDTA 0.1 mM

sample_3: HEXIM, [U-100% 13C; U-100% 15N], 0.5 ± 0.2 mM; 7SK 0.5 ± 0.2 mM; NaCl 70 mM; EDTA 0.1 mM

sample_4: HEXIM 0.5 ± 0.2 mM; 7SK, [U-100% 13C; U-100% 15N], 0.5 ± 0.2 mM; NaCl 70 mM; EDTA 0.1 mM

sample_5: HEXIM 0.5 ± 0.2 mM; 7SK, [U-100% 13C; U-100% 15N], 0.5 ± 0.2 mM; NaCl 70 mM; EDTA 0.1 mM

sample_6: HEXIM, [U-100% 13C; U-100% 15N], 0.5 ± 0.2 mM; 7SK 0.5 ± 0.2 mM; NaCl 70 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 70 mM; pH: 5.6; pressure: 100000 Pa; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	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 HSQC aliphatic	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_6	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

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

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