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- PDB-7z9l: Phen-DC3 intercalation causes hybrid-to-antiparallel transformati... -

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Basic information

Entry
Database: PDB / ID: 7z9l
TitlePhen-DC3 intercalation causes hybrid-to-antiparallel transformation of human telomeric DNA G-quadruplex
ComponentsDNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
KeywordsDNA / G Quadruplex / ligand intercalation / NMR spectroscopy / Mass spectrometry
Function / homologyChem-PQ3 / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGhosh, A. / Trajkovski, M. / Teulade-Fichou, M.P. / Gabelica, V. / Plavec, J.
Funding supportEuropean Union, Slovenia, France, 4items
OrganizationGrant numberCountry
European Union (EU)799695European Union
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ1-1704 Slovenia
Foundation for Medical Research (France)DCM20181039571 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation.
Authors: Ghosh, A. / Trajkovski, M. / Teulade-Fichou, M.P. / Gabelica, V. / Plavec, J.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 5, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0May 15, 2024Group: Data collection / Database references / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.formula / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8382
Polymers7,2881
Non-polymers5511
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Mass: 7287.690 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The DNA is bound to a small molecule named N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide(Phen-DC3). Three letter code (PQ3).
Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-PQ3 / N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide / Phen-DC3


Mass: 550.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H26N6O2 / 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
113isotropic12D 1H-1H TOCSY
123isotropic22D 1H-1H NOESY
141isotropic32D 1H-13C HSQC
152isotropic32D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1200 uM 13C at guanine 23TAG, 95% H2O/5% D2OSite-specifically 13C labeled DNA13C-sample95% H2O/5% D2O
solution2200 uM 15N at guanine 23TAG, 95% H2O/5% D2OSite-specifically 15N labeled DNA15N-sample95% H2O/5% D2O
solution3500 uM Unlabeled 23TAG, 95% H2O/5% D2OUnlabeled DNAUnlabeled-sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uM23TAG13C at guanine1
200 uM23TAG15N at guanine2
500 uM23TAGUnlabeled3
Sample conditionsDetails: 20 mM KCl, 70 mM potassium phosphate buffer with pH 7.0 containing 95% H2O+ 5% D2O and 100% D2O
Ionic strength: 70 mM
Label: 20 mM KCl, 70 mM potassium phosphate buffer with pH 7.0 containing 5% D2O
pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE NEOBrukerAVANCE NEO7001Bruker AVANCE 700 Mhz
Bruker AVANCE IIIBrukerAVANCE III8002Bruker AVANCE 800 Mhz
Bruker AVANCE NEOBrukerAVANCE NEO6003Bruker AVANCE 600 Mhz

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Processing

NMR software
NameVersionDeveloperClassification
Amber20Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
NMRFAM-SPARKY1.414Lee, Woonghee, Marco Tonelli, and John L. Markleychemical shift assignment
TopSpin4.1.3Bruker Biospinprocessing
TopSpin4.1.3Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 497 distance, 24 Planarity, 23 dihedral angle, 16 H bonding
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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