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- PDB-6zl9: Structure of a parallel c-Myc modified with 5' duplex stem-loop o... -

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Basic information

Entry
Database: PDB / ID: 6zl9
TitleStructure of a parallel c-Myc modified with 5' duplex stem-loop overhang
ComponentsDNA (35-MER)
KeywordsDNA / G-quadruplex / Duplex / Quadruplex-Duplex Junction
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsVianney, Y.M. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE 1933/15-1 Germany
CitationJournal: Chemistry / Year: 2020
Title: Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands.
Authors: Vianney, Y.M. / Preckwinkel, P. / Mohr, S. / Weisz, K.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (35-MER)


Theoretical massNumber of molelcules
Total (without water)10,9861
Polymers10,9861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6370 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 11structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (35-MER)


Mass: 10986.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 0.5 mM 0 Nucleic acid, 90% H2O/10% D2O
Details: c-Myc-dup5 dissolved in 90 % 10 mM potassium phosphate buffer + 10 % D2O
Label: mycdup5 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: Nucleic acid / Isotopic labeling: 0
Sample conditionsDetails: Low salt buffer / Ionic strength: 10 mM / Label: mycdup5_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
X-PLOR NIH2.52Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr Analysis2.4.2CCPNdata analysis
CcpNmr Analysis2.4.2CCPNpeak picking
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 11 / Conformers submitted total number: 10

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