BMRB Entry 34553

Name: RNA duplex with a cytosine bulge in complex with berberine
Published: 2021-03-08

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PDB ID: 7a3y
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34553
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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:

RNA duplex with a cytosine bulge in complex with berberine

Deposition date:

2020-08-19

Original release date:

2021-03-08

Authors:

Podbevsek, P.; Plavec, J.

Citation:

Citation: Podbevsek, P.; Plavec, J.. "Interaction between berberine and RNA for the exploration of phytochemicals role" .

Assembly members:

Assembly members:
entity_1, polymer, 13 residues, 4109.478 Da.
entity_2, polymer, 12 residues, 3851.360 Da.
entity_BER, non-polymer, 336.361 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GCAGCUCGUCCUG
entity_2: CAGGAUAGCUGC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	116

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
3	unit_3	3

Entities:

Entity 1, unit_1 13 residues - 4109.478 Da.

1

G

C

A

G

C

U

C

G

U

C

2

C

U

G

Entity 2, unit_2 12 residues - 3851.360 Da.

1

C

A

G

A

U

A

G

C

U

2

G

C

Entity 3, unit_3 - C20 H18 N O4 - 336.361 Da.

1

BER

Samples:

sample_1: RNA-A chain A 0.3 mM; RNA-A chain B 0.3 mM; sodium chloride 100 mM; sodium phosphate 10 mM; EDTA 1 mM

sample_conditions_1: ionic strength: 110 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CcpNmr Analysis v3.0.1, CCPN - chemical shift assignment

Amber v20, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

NMR spectrometers:

Varian VNMRS800 800 MHz