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- PDB-6ia4: Human telomeric G-quadruplex with 8-oxo-G substitution in the out... -

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Basic information

Entry
Database: PDB / ID: 6ia4
TitleHuman telomeric G-quadruplex with 8-oxo-G substitution in the outer G-quartet
ComponentshTel-oxoG21
KeywordsDNA / Human telomere / oxidative stress / G-quadruplex / NMR.
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBielskute, S. / Plavec, J. / Podbevsek, P.
Funding support Slovenia, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ3-6800 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Impact of Oxidative Lesions on the Human Telomeric G-Quadruplex.
Authors: Bielskute, S. / Plavec, J. / Podbevsek, P.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 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 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 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:
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Assembly

Deposited unit
A: hTel-oxoG21


Theoretical massNumber of molelcules
Total (without water)7,6081
Polymers7,6081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area520 Å2
ΔGint3 kcal/mol
Surface area4110 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain hTel-oxoG21


Mass: 7607.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 1 mM DNA, 90% H2O/10% D2O / Label: hTel-oxoG21 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: DNA / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 70 mM / Label: standard / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent DDR2 / Manufacturer: Agilent / Model: DDR2 / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 12

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