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- PDB-5lig: G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-... -

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Basic information

Entry
Database: PDB / ID: 5lig
TitleG-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2
ComponentsDNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')
KeywordsDNA / G-QUADRUPLEX / C-MYC PROMOTER / LIGAND / DAOTA-M2
Function / homologyChem-6XM / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKotar, A. / Wang, B. / Shivalingam, A. / Gonzalez-Garcia, J. / Vilar, R. / Plavec, J.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex.
Authors: Kotar, A. / Wang, B. / Shivalingam, A. / Gonzalez-Garcia, J. / Vilar, R. / Plavec, J.
History
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Feb 14, 2018Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.manufacturer
Revision 2.0Mar 7, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description
Category: atom_site / database_PDB_caveat / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula
Revision 2.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.2May 15, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,0923
Polymers6,0711
Non-polymers1,0212
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4060 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 6070.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-6XM / 8,12-bis(2-morpholinoethyl)-8H-benzo[ij]xantheno[1,9,8-cdef][2,7]naphthyridin-12-iumhexafluorophosphate


Mass: 510.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H34N4O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
213anisotropic22D 1H-1H TOCSY
123anisotropic22D 1H-1H TOCSY
231anisotropic12D 1H-1H NOESY
142anisotropic22D 1H-1H NOESY
253anisotropic12D 1H-1H DQF COSY
263anisotropic12D 1H-31P COSY
274anisotropic113C HSQC
284anisotropic115N HSQC
292anisotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2, 90% H2O/10% D2Osample190% H2O/10% D2O
solution20.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 10 mM LITHIUM CACODYLATE, 0.4 mM DAOTA-M2, 90% H2O/10% D2Osample290% H2O/10% D2O
solution30.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2, 100% D2Osample3100% D2O
solution40.2 mM U-8% 15N, U-8 %13C DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2, 90% H2O/10% D2Osample490% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMDNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')natural abundance1
100 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
0.4 mMDAOTA-M2natural abundance1
0.2 mMDNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')natural abundance2
100 mMpotassium chloridenatural abundance2
10 mMLITHIUM CACODYLATEnatural abundance2
0.4 mMDAOTA-M2natural abundance2
0.2 mMDNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')natural abundance3
100 mMpotassium chloridenatural abundance3
20 mMpotassium phosphatenatural abundance3
0.4 mMDAOTA-M2natural abundance3
0.2 mMDNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')U-8% 15N, U-8 %13C4
100 mMpotassium chloridenatural abundance4
20 mMpotassium phosphatenatural abundance4
0.4 mMDAOTA-M2natural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1145 mMconditions_17.0 1 atm278 K
2140 mMconditions_27.0 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Varian Uniform NMR SystemVarianUniform NMR System8002

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Processing

NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
VNMRVariancollection
VNMRVarianprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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