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- PDB-7el7: NMR solution structure of the 1:1 complex of a quadruplex-duplex ... -

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Basic information

Entry
Database: PDB / ID: 7el7
TitleNMR solution structure of the 1:1 complex of a quadruplex-duplex hybrid MYT1L and a platinum(II) ligand L1Pt(dien)
ComponentsG-quadruplex DNA MYT1L
KeywordsDNA / G-quadruplex / Quadruplex-Duplex Hybrid / Complex
Function / homologyChem-J70 / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, L.-Y. / Liu, W. / Mao, Z.-W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Spatial Matching Selectivity and Solution Structure of Organic-Metal Hybrid to Quadruplex-Duplex Hybrid.
Authors: Liu, L.Y. / Wang, K.N. / Liu, W. / Zeng, Y.L. / Hou, M.X. / Yang, J. / Mao, Z.W.
History
DepositionApr 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-quadruplex DNA MYT1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8722
Polymers9,2171
Non-polymers6561
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain G-quadruplex DNA MYT1L


Mass: 9216.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-J70 / Pt(diethylenetriamine)(2-(pyridin-4-ylmethyl)benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetraone)


Mass: 655.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N6O4Pt / 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 1H-1H NOESY
221isotropic12D 1H-1H NOESY
331isotropic12D 1H-1H NOESY
142isotropic12D 1H-1H NOESY
252isotropic12D 1H-1H NOESY
362isotropic12D 1H-1H NOESY
171isotropic12D 1H-1H TOCSY
182isotropic12D 1H-1H TOCSY
292isotropic12D 1H-1H TOCSY
3102isotropic12D 1H-1H TOCSY
1111isotropic12D 1H-1H COSY
1122isotropic12D 1H-1H COSY
2132isotropic12D 1H-1H COSY
3142isotropic12D 1H-1H COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.5 mM no G-quadruplex DNA MYT1L, 90% H2O/10% D2O1_sample90% H2O/10% D2O
solution21.5 mM no G-quadruplex DNA MYT1L, 100% D2O2_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMG-quadruplex DNA MYT1Lno1
1.5 mMG-quadruplex DNA MYT1Lno2
Sample conditions

Ionic strength: 40 mM / Ionic strength err: 0.2 / pH: 7.0 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature err: 0.2

Conditions-IDLabelTemperature (K)
11298 K
22288 K
33278 K

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NMR measurement

NMR spectrometerType: Bruker AVIII / Manufacturer: Bruker / Model: AVIII / Field strength: 600 MHz

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Processing

SoftwareName: CNS / Classification: refinement
NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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