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- PDB-7w0x: Tetrameric antiparallel G-quadruplex formed by natural human telo... -

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Basic information

Entry
Database: PDB / ID: 7w0x
TitleTetrameric antiparallel G-quadruplex formed by natural human telomeric sequence
ComponentsDNA (5'-D(*GP*GP*GP*TP*TP*A)-3')
KeywordsDNA / G-quadruplex / Antiparallel / C2-symmetry / Human telomere
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJing, H.T. / Fu, W.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)E06ZN11301 China
CitationJournal: To Be Published
Title: NMR structure of an alternating antiparallel tetrameric G-quadruplex assembled by the single-repeat of human telomeric DNA d(GGGTTA)
Authors: Zhang, N. / Jing, H.T. / Fu, W.Q.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 19, 2022ID: 6IMS
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1May 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:
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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*TP*TP*A)-3')
B: DNA (5'-D(*GP*GP*GP*TP*TP*A)-3')
C: DNA (5'-D(*GP*GP*GP*TP*TP*A)-3')
D: DNA (5'-D(*GP*GP*GP*TP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)7,4574
Polymers7,4574
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2410 Å2
ΔGint-16 kcal/mol
Surface area3670 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*GP*GP*TP*TP*A)-3')


Mass: 1864.252 Da / Num. of mol.: 4 / 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 NOESY
222isotropic22D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM NA potassium phosphate, 6 mM NA DNA (5'-D(*GP*GP*GP*TP*TP*A)-3'), 100% D2OD2O100% D2O
solution220 mM NA potassium phosphate, 6 mM NA DNA (5'-D(*GP*GP*GP*TP*TP*A)-3'), 95% H2O/5% D2OH2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMpotassium phosphateNA1
6 mMDNA (5'-D(*GP*GP*GP*TP*TP*A)-3')NA1
20 mMpotassium phosphateNA2
6 mMDNA (5'-D(*GP*GP*GP*TP*TP*A)-3')NA2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMconditions_16.81 atm310 K
250 mMconditions_26.81 atm288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 2
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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