BMRB Entry 34553

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:
Data typeCount
1H chemical shifts116

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33

Entities:

Entity 1, unit_1 13 residues - 4109.478 Da.

1   GCAGCUCGUC
2   CUG

Entity 2, unit_2 12 residues - 3851.360 Da.

1   CAGGAUAGCU
2   GC

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:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_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