BMRB Entry 25826

Name: solution structure of microRNA 20b pre-element
Published: 2016-04-12

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PDB ID: 2n7x
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25826
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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 microRNA 20b pre-element

Deposition date:

2015-09-25

Original release date:

2016-04-12

Authors:

Yang, Fan; Chen, Yu; Varani, Gabriele

Citation:

Citation: Chen, Yu; Zubovic, Lorena; Yang, Fan; Godin, Katherine; Pavelitz, Tom; Castellanos, Javier; Macchi, Paolo; Varani, Gabriele. "Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer" Nucleic Acids Res. 44, 4381-4395 (2016).
PubMed: 27001519

Assembly members:

Assembly members:
miR-20b, polymer, 23 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: T7 in vitro transcription Host organism: NA Vector: NA

Entity Sequences (FASTA):

Entity Sequences (FASTA):
miR-20b: GGUAGUUUUGGCAUGACUCU ACC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	153
1H chemical shifts	175

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	miR-20b	1

Entities:

Entity 1, miR-20b 23 residues - Formula weight is not available

1

G

U

A

G

U

G

2

G

C

A

U

G

A

C

U

C

U

3

A

C

Samples:

sample_1: miR-20b 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; H2O 90%; D2O 10%

sample_2: miR-20b 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; D2O 100%

sample_3: miR-20b, [U-99% 13C; U-99% 15N], 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; D2O 100%

sample_4: miR-20b, [U-99% 13C; U-99% 15N], 1 mM; sodium phosphate 10 mM; sodium chloride 20 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 279 K

sample_conditions_2: pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_3: pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_4: pH: 6.5; pressure: 1 atm; temperature: 279 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_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_3
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_4

Software:

TOPSPIN, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

CcpNMR, CCPN - chemical shift assignment, data analysis, peak picking

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

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

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz