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- PDB-6gzn: Adenine-driven structural switch from two- to three-quartet DNA G... -

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Basic information

Entry
Database: PDB / ID: 6gzn
TitleAdenine-driven structural switch from two- to three-quartet DNA G-quadruplex
ComponentsDNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3')
KeywordsDNA / G-quadruplex / basket-type topology / RANKL gene / osteoporosis
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLenarcic Zivkovic, M. / Rozman, J. / Plavec, J.
Funding support Slovenia, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
Slovenian Research AgencyJ3-7245 Slovenia
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Adenine-Driven Structural Switch from a Two- to Three-Quartet DNA G-Quadruplex.
Authors: Lenarcic Zivkovic, M. / Rozman, J. / Plavec, J.
History
DepositionJul 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 21, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / 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_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_seq_map_depositor_info
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5May 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 1.6May 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,4101
Polymers6,4101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3780 Å2
MethodPISA
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(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3')


Mass: 6410.127 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
111isotropic22D 1H-1H NOESY
122isotropic12D 1H-1H TOCSY
132isotropic12D DQF-COSY
141isotropic12D 1H-13C HSQC aliphatic
151isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2ORan4_H2090% H2O/10% D2O
solution20.8 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3'), 100% D2ORan4_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMDNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3')natural abundance1
0.8 mMDNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3')natural abundance2
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DD2AgilentDD26001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
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: 10

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