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- PDB-6jwd: structure of RET G-quadruplex in complex with berberine -

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Basic information

Entry
Database: PDB / ID: 6jwd
Titlestructure of RET G-quadruplex in complex with berberine
ComponentsDNA (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')
KeywordsDNA / RET / G-quadruplex / berberine
Function / homologyBERBERINE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, F. / Wang, C. / Liu, Y. / Lan, W.X. / Li, Y.M. / Wang, R.X. / Cao, C.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2020
Title: Colchicine selective interaction with oncogene RET G-quadruplex revealed by NMR.
Authors: Wang, F. / Wang, C. / Liu, Y. / Lan, W. / Han, H. / Wang, R. / Huang, S. / Cao, C.
#1: Journal: Nucleic Acids Res. / Year: 2011
Title: Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence.
Authors: Tong, X. / Lan, W. / Zhang, X. / Wu, H. / Liu, M. / Cao, C.
History
DepositionApr 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7302
Polymers6,3941
Non-polymers3361
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: one-dimensional NMR detected the Hoogsteen hydrogen bonds formed in G-quadruplex
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area600 Å2
ΔGint5 kcal/mol
Surface area3640 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')


Mass: 6394.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-BER / BERBERINE / Berberine


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
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
111anisotropic12D 1H-1H NOESY
121anisotropic12D 1H-1H TOCSY
131anisotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 1.4 mM RET G4-DNA, 1.68 mM BERBERINE, 20 mM Potassium Phosphate Monobasic, 80 mM potassium chloride, 90% H2O/10% D2O
Label: RET G4-DNA sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMRET G4-DNAnatural abundance1
1.68 mMBERBERINEnatural abundance1
20 mMPotassium Phosphate Monobasicnatural abundance1
80 mMpotassium chloridenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: RET G4 berberine solution complex / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Agilent INOVA / Manufacturer: Agilent / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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