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- PDB-6ccw: Hybrid-2 form Human Telomeric G Quadruplex in Complex with Epiber... -

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Basic information

Entry
Database: PDB / ID: 6ccw
TitleHybrid-2 form Human Telomeric G Quadruplex in Complex with Epiberberine
ComponentsDNA (26-MER)
KeywordsDNA / G-Quadruplex / Complex / Telomere
Function / homologyEpiberberine / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLin, C. / Yang, D.Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Molecular Recognition of the Hybrid-2 Human Telomeric G-Quadruplex by Epiberberine: Insights into Conversion of Telomeric G-Quadruplex Structures.
Authors: Lin, C. / Wu, G. / Wang, K. / Onel, B. / Sakai, S. / Shao, Y. / Yang, D.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Dec 18, 2019Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 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
Revision 2.2May 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

Downloads & links

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Assembly

Deposited unit
A: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5372
Polymers8,2001
Non-polymers3361
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain DNA (26-MER)


Mass: 8200.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-EWV / Epiberberine / 8,9-dimethoxy-11,12-dihydro-2H-[1,3]dioxolo[4,5-h]isoquinolino[2,1-b]isoquinolin-13-ium


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H NOESY
121anisotropic12D 1H-1H TOCSY
231anisotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 880 uM DNA (26-MER), 880 uM epiberberine, 90% H2O/10% D2O
Label: NMR-Sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
880 uMDNA (26-MER)natural abundance1
880 uMepiberberinenatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mMCondition-257 1 atm298 K
2100 mMCondition-157 1 atm288 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
Insight IIAccelrys Software Inc.structure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 15

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