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- PDB-6v0l: PDGFR-b Promoter Forms a G-Vacancy Quadruplex that Can be Complem... -

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Basic information

Entry
Database: PDB / ID: 6v0l
TitlePDGFR-b Promoter Forms a G-Vacancy Quadruplex that Can be Complemented by dGMP: Molecular Structure and Recognition of Guanine Derivatives and Metabolites
ComponentsDNA (5'-D(*(3D1)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*A)-3')
KeywordsDNA / G-quadruplex / PDGFR-b / Promoter
Function / homology2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsWang, K.B. / Dickerhoff, J. / Wu, G. / Yang, D.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01CA177585 United States
German Research Foundation (DFG)427347592 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: PDGFR-beta Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs.
Authors: Wang, K.B. / Dickerhoff, J. / Wu, G. / Yang, D.
History
DepositionNov 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: DNA (5'-D(*(3D1)P*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)6,2772
Polymers5,9301
Non-polymers3471
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area830 Å2
ΔGint9 kcal/mol
Surface area3720 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(*(3D1)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*A)-3')


Mass: 5929.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
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
311isotropic22D 1H-1H TOCSY
121isotropic22D 1H-1H NOESY
261isotropic22D 1H-1H NOESY
351isotropic22D 1H-1H NOESY
331isotropic22D 1H-1H COSY
241isotropic22D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP), 90% H2O/10% D2O
Label: 1H_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 3600 uM
Component: DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP)
Isotopic labeling: 1H
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMconditions_17.0 760 mmHg288 K
250 mMconditions_27 760 mmHg298 K
350 mMconditions_37 760 mmHg278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
TopSpinBruker Biospinprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics3
simulated annealing2molecular dynamics
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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