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- PDB-9kg8: Solution structure of the 2:1 berberine- hTERT-G4 complex -

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Basic information

Entry
Database: PDB / ID: 9kg8
TitleSolution structure of the 2:1 berberine- hTERT-G4 complex
ComponentsDNA (5'-D(*AP*AP*AP*GP*GP*GP*TP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*CP*GP*GP*GP*GP*TP*T)-3')
KeywordsDNA / hTERT promoter / G-quadruplex / NMR solution structure
Function / homologyBERBERINE / DNA / 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)82173707 China
CitationJournal: To Be Published
Title: G146A Mutation in hTERT Promoter Induces a Distinct G-Quadruplex That Activates hTERT Transcription: Structure Determination and Its Potential as a Drug Target
Authors: Zhang, Y.Q. / Gu, W. / He, S.H. / Cheng, R.S. / Chen, Z.Y. / Yan, T.D. / Kong, L.Y. / Wang, K.B.
History
DepositionNov 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,2453
Polymers7,5721
Non-polymers6732
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*AP*AP*AP*GP*GP*GP*TP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*CP*GP*GP*GP*GP*TP*T)-3')


Mass: 7571.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18NO4
Has ligand of interestN
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
221isotropic12D 1H-1H NOESY
331isotropic12D 1H-1H NOESY
241isotropic12D DQF-COSY
251isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 1.434 mM BER-mut-hTERT-G4, 90% H2O/10% D2O / Label: none / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.434 mM / Component: BER-mut-hTERT-G4 / Isotopic labeling: none
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMConditions_171 atm288 K
210 mMConditions_271 atm298 K
310 mMConditions_371 atm298 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
TopSpinBruker Biospincollection
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYWoonghee Leepeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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