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- PDB-9jo0: Solution structure of free BLM promoter G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 9jo0
TitleSolution structure of free BLM promoter G-quadruplex
ComponentsDNA (5'-D(*TP*GP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*AP*T)-3')
KeywordsDNA / BLM promoter / G-quadruplex / NMR solution structure
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsWang, K.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82322065 China
CitationJournal: To Be Published
Title: BLM G-quadruplex stabilizers synergize with PARP inhibitor to kill BRCA wild-type colon cancer cells
Authors: Wang, Y.Y. / Bian, Y.T. / Chen, X.Y. / Li, J.Z. / Liu, Y.S. / Kong, L.Y. / Wang, K.B.
History
DepositionSep 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DNA (5'-D(*TP*GP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,6981
Polymers6,6981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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(*TP*GP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*AP*T)-3')


Mass: 6698.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationN

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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
222isotropic12D 1H-1H NOESY
332isotropic12D 1H-1H NOESY
242isotropic12D 1H-13C HSQC
252isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.62 mM None BLM_Pu21T, 90% H2O/10% D2Onone90% H2O/10% D2O
solution21.93 mM None BLM_Pu21T, 90% H2O/10% D2Onone90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.62 mMBLM_Pu21TNone1
1.93 mMBLM_Pu21TNone2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMConditions_171 atm288 K
250 mMConditions_271 atm298 K
350 mMConditions_371 atm308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz / Details: QCI cryoprobe

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYWoonghee Leepeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
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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