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- PDB-7kbw: Solution structure of the major MYC promoter G-quadruplex with a ... -

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Basic information

Entry
Database: PDB / ID: 7kbw
TitleSolution structure of the major MYC promoter G-quadruplex with a wild-type flanking in complex with NSC85697, a quinoline derivative
ComponentsMyc2345
KeywordsDNA / G-QUADRUPLEX DNA / DRUG-DNA COMPLEX
Function / homologyChem-WAM / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsDickerhoff, J. / Yang, D.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA177585 United States
German Research Foundation (DFG)427347592 Germany
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes.
Authors: Dickerhoff, J. / Dai, J. / Yang, D.
History
DepositionOct 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myc2345
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7043
Polymers7,0341
Non-polymers6712
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain Myc2345


Mass: 7033.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-WAM / 2-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]-1-methyl-quinoline-4-carboxamide


Mass: 335.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N2O3 / 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
221isotropic12D NOESY
331isotropic12D NOESY
341isotropic12D DQF-COSY
151isotropic12D 1H-13C HSQC aromatic

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Sample preparation

DetailsType: solution
Contents: 0.8 mM Myc2345, 2.4 mM NSC85697, 10 mM potassium phosphate, 90% H2O/10% D2O
Label: Myc2345+ligand / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMMyc2345natural abundance1
2.4 mMNSC85697natural abundance1
10 mMpotassium phosphatenatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMconditions_171 atm298 K
210 mMconditions_271 atm288 K
310 mMconditions_371 atm308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
Refinement
MethodSoftware ordinal
simulated annealing2
simulated annealing5
molecular dynamics1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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