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- PDB-7msv: Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadrup... -

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Entry
Database: PDB / ID: 7msv
TitleSolution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter
ComponentsDNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*A)-3')
KeywordsDNA / G-quadruplex / promoter / Guanine metabolite
Function / homologyBERBERINE / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsWang, K.B. / Dickerhoff, J. / Yang, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA177585 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-beta Promoter.
Authors: Wang, K.B. / Dickerhoff, J. / Yang, D.
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 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
X: DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0304
Polymers6,0101
Non-polymers1,0203
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1690 Å2
ΔGint21 kcal/mol
Surface area3990 Å2
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(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*A)-3')


Mass: 6009.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxyguanosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical ChemComp-BER / BERBERINE / Berberine


Mass: 336.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18NO4 / Comment: alkaloid*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic22D 1H-1H NOESY
221anisotropic22D 1H-1H NOESY
331anisotropic22D 1H-1H NOESY
141anisotropic22D 1H-13C HSQC
151anisotropic22D 1H-1H TOCSY
162anisotropic21D GEJRSE HMQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.5 mM BER-dGMP-Pu19m2, 90% H2O/10% D2OThe ternary complex of berberine bound to dGMP fill-in G4 sample was used for 2D NMR data collection.NO90% H2O/10% D2O
solution29 mM [U-100% 13C; U-100% 15N] dGMP, 90% H2O/10% D2OThe dGMP was involved in the G4 formation in the ternary complex and was confirmed by using 13C-15N-labeled dGMP with 15N-edited experiments13C_15N_dGMP90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMBER-dGMP-Pu19m2natural abundance1
9 mMdGMP[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMconditions_17.0 760 mmHg298 K
250 mMconditions_27.0 760 mmHg288 K
350 mMconditions_37.0 760 mmHg308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AV 500BrukerAV 5005001
Bruker AV 800BrukerAV 8008002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRFAM-SPARKYLee W, Tonelli M, Markley JL.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 4
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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