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- PDB-7a3y: RNA duplex with a cytosine bulge in complex with berberine -

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Basic information

Entry
Database: PDB / ID: 7a3y
TitleRNA duplex with a cytosine bulge in complex with berberine
Components
  • RNA-A chain A
  • RNA-A chain B
KeywordsRNA / berberine / cytosine bulge
Function / homologyBERBERINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsPodbevsek, P. / Plavec, J.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Interaction between berberine and RNA for the exploration of phytochemicals role
Authors: Podbevsek, P. / Plavec, J.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-A chain A
B: RNA-A chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2973
Polymers7,9612
Non-polymers3361
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR observables
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1910 Å2
ΔGint-7 kcal/mol
Surface area4820 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA-A chain A


Mass: 4109.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA-A chain B


Mass: 3851.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.3 mM RNA-A chain A, 0.3 mM RNA-A chain B, 100 mM sodium chloride, 10 mM sodium phosphate, 1 mM EDTA, 90% H2O/10% D2O
Details: Equimolar ammounts of RNA and berberine in solution
Label: complex / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMRNA-A chain Anatural abundance1
0.3 mMRNA-A chain Bnatural abundance1
100 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
1 mMEDTAnatural abundance1
Sample conditionsIonic strength: 110 mM / Label: c1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS800 / Manufacturer: Varian / Model: VNMRS800 / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis3.0.1CCPNchemical shift assignment
Amber20Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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