BMRB Entry 31061

Name: Structure of pre-miR-31 reveals an active role in Dicer processing
Published: 2023-02-14

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PDB ID: 8fcs
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31061
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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 pre-miR-31 reveals an active role in Dicer processing

Deposition date: 2022-12-01 Original release date: 2023-02-14

Authors: Kotar, A.; Ma, S.; Keane, S.

Citation: Kotar, A.; Ma, S.; Keane, S.. "Structure of pre-miR-31 reveals an active role in Dicer processing" .

Assembly members:
entity_1, polymer, 71 residues, 22872.592 Da.

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

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGAGAGGAGGCAAGAUGCUG GCAUAGCUGUUGAACUGGGA ACCUGCUAUGCCAACAUAUU GCCAUCUUUCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	54
1H chemical shifts	329

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 71 residues - 22872.592 Da.

1

G

A

G

A

G

A

G

2

C

A

G

A

U

G

C

U

G

3

G

C

A

U

A

G

C

U

G

U

4

U

G

A

C

U

G

A

5

A

C

U

G

C

U

A

U

G

6

C

A

C

A

U

A

U

7

G

C

A

U

C

U

C

8

C

Samples:

sample_1: RNA (71-MER) 0.5 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_2: RNA (71-MER), A2rGr-labeled, 0.45 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_3: RNA (71-MER), A2rGrUr-labeled, 0.45 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_4: RNA (71-MER), AHCH-labeled, 0.45 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_5: RNA (71-MER), GHU6r-labeled, 0.45 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_6: RNA (71-MER), 15N/13C AG-labeled, 0.48 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_7: RNA (71-MER), 15N AU-labeled, 0.56 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_8: RNA (71-MER), 15N/13C AG-labeled_2, 0.48 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_9: RNA (71-MER), 15N/13C AG-labeled_3, 0.40 mM; KPhosphate buffer 50 mM; MgCl2 1 mM

sample_10: RNA (71-MER), 15N/13C AG-labeled_4, 0.60 mM; KPhosphate buffer 50 mM; MgCl2 1 mM; Pf1 phage 10 mg/mL

sample_conditions_1: ionic strength: 0.0025 M; pH: 7.5 pD; pressure: 1 atm; temperature: 310 K

sample_conditions_2: ionic strength: 0.0025 M; pH: 7.5; pressure: 1 atm; temperature: 310 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-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1
2D 1H-13C IPAP-HSQC	sample_9	isotropic	sample_conditions_2
2D 1H-15N BESTsellr HNN COSY	sample_6	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_7	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_6	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C IPAP-HSQC	sample_10	anisotropic	sample_conditions_2
2D 1H-13C HSQC	sample_8	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

NMRFx, Johnson - processing

NMRViewJ v9.2.0-b24, Johnson - chemical shift assignment

NMRViewJ, Johnson - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE NEO 600 MHz
Bruker AVANCE NEO 800 MHz