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- PDB-6m05: Trimolecular G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 6m05
TitleTrimolecular G-quadruplex
ComponentsDNA (5'-D(*GP*TP*TP*AP*GP*G)-3')
KeywordsDNA / Trimolecular G-quadruplex / Human / Tolerance
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJing, H.T. / Fu, W.Q. / Zhang, N.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1932157 China
National Natural Science Foundation of China (NSFC)21372223 China
National Natural Science Foundation of China (NSFC)U1232145 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance.
Authors: Jing, H. / Fu, W. / Hu, W. / Xu, S. / Xu, X. / He, M. / Liu, Y. / Zhang, N.
History
DepositionFeb 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: 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: 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 1.3May 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: DNA (5'-D(*GP*TP*TP*AP*GP*G)-3')
B: DNA (5'-D(*GP*TP*TP*AP*GP*G)-3')
C: DNA (5'-D(*GP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,5933
Polymers5,5933
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: TOCSY (Total Correlation Spectroscopy) , 13C,1H (Heteronculear Single Quantum Coherence), 15N,1H (Heteronculear Single Quantum Coherence).
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1230 Å2
ΔGint0 kcal/mol
Surface area3910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*GP*TP*TP*AP*GP*G)-3')


Mass: 1864.252 Da / Num. of mol.: 3 / 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
152isotropic12D 1H-1H NOESY
161isotropic12D 1H-15N HSQC
172isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution18 mM DNA (5'-D(*GP*TP*TP*AP*GP*G)-3'), 20 mM sodium phosphate, 100 mM sodium chloride, 10 % v/v D2O, 90 v/v H2O, 90% H2O/10% D2OH2O_sample90% H2O/10% D2O
solution28 mM DNA (5'-D(*GP*TP*TP*AP*GP*G)-3'), 100 mM sodium chloride, 20 mM sodium phosphate, 100 % v/v D2O, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
8 mMDNA (5'-D(*GP*TP*TP*AP*GP*G)-3')natural abundance1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
10 % v/vD2Onatural abundance1
90 v/vH2Onatural abundance1
8 mMDNA (5'-D(*GP*TP*TP*AP*GP*G)-3')natural abundance2
100 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
100 % v/vD2Onatural abundance2
Sample conditionsIonic strength: 100 mM / Label: 288K_condition / pH: 6.8 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH3.0.3Schwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr Analysis2.4.2CCPNchemical shift assignment
TopSpin3.6.2Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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