BMRB Entry 27226

Name: hsa-miR-34a-mSIRT1_bulge
Published: 2020-05-21

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27226

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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:

hsa-miR-34a-mSIRT1_bulge

Deposition date:

2017-08-19

Original release date:

2020-05-21

Authors:

Baronti, Lorenzo; Steiner, Emilie; Schlagnitweit, Judith; Petzold, Katja

Citation:

Citation: Baronti, Lorenzo; Guzzetti, Ileana; Ebrahimi, Parisa; Friebe Sandoz, Sarah; Steiner, Emilie; Schlagnitweit, Judith; Fromm, Bastian; Silva, Luis; Fontana, Carolina; Chen, Alan; Petzold, Katja. "Base-pair Conformational Switch Modulates miR-34a Targeting of Sirt1 mRNA" Nature 583, 139-144 (2020).
PubMed: 32461691

Assembly members:

Assembly members:
hsa-miR-34a-mSIRT1_bulge, polymer, 28 residues, 8458.4 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: enzymatic semisynthesis Host organism: T7 in vitro transcritpion Vector: DNA template

Entity Sequences (FASTA):

Entity Sequences (FASTA):
hsa-miR-34a-mSIRT1_bulge: GGCACCAUUACUGCUUCGGC AGUGUGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	67
15N chemical shifts	54
1H chemical shifts	94

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	hsa-miR-34a-mSIRT1_bulge	1

Entities:

Entity 1, hsa-miR-34a-mSIRT1_bulge 28 residues - 8458.4 Da.

Nts 14-19 constitute a synthetic cUUCGg motif. Nts 1-3 and 26-28 synthetic closing stem. Nts 20-25 hsa-miR-34a-5p and nts 4-13 mSIRT1 side of the hetero-duplex, respectively.

1

G

C

A

C

A

U

A

2

C

U

G

C

U

C

G

C

3

A

G

U

G

U

G

C

Samples:

sample_1: hsa-miR-34a-mSIRT1_bulge, [U-100% 13C; U-100% 15N], 750 uM; H2O 90%; D2O, [U-2H], 10%; sodium phosphate 15 mM; sodium chloride 25 mM; EDTA 0.1 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 295.4 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D HNN COSY	sample_1	isotropic	sample_conditions_1
3D HCN	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN vv 3.2, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance III HD 600 MHz