BMRB Entry 30257

Name: Structure of wild type pre-miR21 apical loop
Published: 2017-06-08

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PDB ID: 5uzt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30257
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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:

Structure of wild type pre-miR21 apical loop

Deposition date:

2017-02-27

Original release date:

2017-06-08

Authors:

Shortridge, M.; Varani, G.

Citation:

Citation: Shortridge, M.; Walker, M.; Pavelitz, T.; Chen, Y.; Yang, W.; Varani, G.. "A macrocyclic peptide ligand binds the oncogenic microRNA-21 precursor and suppresses Dicer processing." ACS Chem. Biol. 12, 1611-1620 (2017).
PubMed: 28437065

Assembly members:

Assembly members:
entity_1, polymer, 31 residues, 9912.896 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: GGUGUUGACUGUUGAAUCUC AUGGCAACACC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	129
1H chemical shifts	180

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 31 residues - 9912.896 Da.

1

G

U

G

U

G

A

C

U

2

G

U

G

A

U

C

U

C

3

A

U

G

C

A

C

A

C

4

C

Samples:

sample_1: EDTA 0.01 mM; potassium phosphate 10 mM; pre-miR-21 1.1 mM; sodium chloride 10 mM

sample_2: EDTA 0.01 mM; potassium phosphate 10 mM; pre-miR-21 1.1 mM; sodium chloride 10 mM

sample_3: EDTA 0.01 mM; potassium phosphate 10 mM; pre-miR-21, [U-99% 13C; U-99% 15N], 0.5 mM; sodium chloride 10 mM

sample_4: EDTA 0.01 g/L; potassium phosphate 10 mM; pre-miR-21, [U-99% 13C; U-99% 15N], 0.5 mM; sodium chloride 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

Analysis, CCPN - chemical shift assignment

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

SPARKY, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - processing

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

NMR spectrometers:

Bruker DRX 500 MHz
Bruker AvanceIII 800 MHz