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- PDB-5z80: Solution structure for the 1:1 complex of a platinum(II)-based tr... -

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Basic information

Entry
Database: PDB / ID: 5z80
TitleSolution structure for the 1:1 complex of a platinum(II)-based tripod bound to a hybrid-1 human telomeric G-quadruplex
ComponentsG-quadruplex DNA (26-MER)
KeywordsDNA / Intramolecular G-quadruplex / Human Telomeric G-quadruplex / Platinum(II) complex / Ligand-DNA complex
Function / homologyChem-9F0 / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsLiu, W.T. / Zhong, Y.F. / Liu, L.Y. / Zeng, W.J. / Wang, F.Y. / Yang, D.Z. / Mao, Z.W.
Funding support China, 4items
OrganizationGrant numberCountry
973 program2014CB845604 and 2015CB856301 China
National Science Foundation of China21231007 and 21572282 China
Ministry of Education of ChinaIRT-17R111 China
Science and Technology Planning Project of Guangdong Province2013B051000047 and 207999 China
CitationJournal: Nat Commun / Year: 2018
Title: Solution structures of multiple G-quadruplex complexes induced by a platinum(II)-based tripod reveal dynamic binding
Authors: Liu, W. / Zhong, Y.F. / Liu, L.Y. / Shen, C.T. / Zeng, W. / Wang, F. / Yang, D. / Mao, Z.W.
History
DepositionJan 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-quadruplex DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6082
Polymers8,2361
Non-polymers1,3711
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5710 Å2
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 G-quadruplex DNA (26-MER)


Mass: 8236.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-9F0 / 4-[1-(2,5,8-triazonia-1$l^4-platinabicyclo[3.3.0]octan-1-yl)pyridin-1-ium-4-yl]-N,N-bis[4-[1-(2,5,8-triazonia-1$l^4-platinabicyclo[3.3.0]octan-1-yl)pyridin-1-ium-4-yl]phenyl]aniline


Mass: 1371.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H63N13Pt3 / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic22D 1H-1H NOESY
121anisotropic22D 1H-1H TOCSY
131anisotropic22D 1H-1H COSY
241anisotropic12D 1H-1H NOESY
251anisotropic12D 1H-1H TOCSY
261anisotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM G-quadruplex DNA (26-MER), 1.0 mM Pt-tripod, 70 mM potassium chloride, 25 mM potassium phosphate, 90% H2O/10% D2O
Label: 2D_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMG-quadruplex DNA (26-MER)natural abundance1
1.0 mMPt-tripodnatural abundance1
70 mMpotassium chloridenatural abundance1
25 mMpotassium phosphatenatural abundance1
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
125 Celsius experiments95 mMconditions_17.0 AMBIENT MBAR mbar298 K
215 Celsius experiments95 mMconditions_27.0 AMBIENT MBAR mbar288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVIIIBrukerAVIII6001
Bruker AVIIIBrukerAVIII7002

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Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospinprocessing
SPARKYGoddardchemical shift assignment
X-PLORBrungerstructure calculation
SPARKYGoddardpeak picking
X-PLORBrungerrefinement
DISCOVERAccelrys Software Inc.refinement
Refinement
MethodSoftware ordinal
simulated annealing4
DGSA-distance geometry simulated annealing5
molecular dynamics6
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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