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- PDB-2hy9: Human telomere DNA quadruplex structure in K+ solution hybrid-1 form -

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Basic information

Entry
Database: PDB / ID: 2hy9
TitleHuman telomere DNA quadruplex structure in K+ solution hybrid-1 form
ComponentsDNA (26-MER)
KeywordsDNA / G-quadruplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsDai, J. / Punchihewa, C. / Jones, R.A. / Hurley, L. / Yang, D.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation.
Authors: Dai, J. / Punchihewa, C. / Ambrus, A. / Chen, D. / Jones, R.A. / Yang, D.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 17, 2014Group: Other / Structure summary
Revision 1.4May 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
1: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)8,2361
Polymers8,2361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain DNA (26-MER)


Mass: 8236.324 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (Human).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 0.1-2.5mM oligonucleotide, 25mM phosphate buffer K, 70mM KCl, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 70mM KCl, 25mM K-phosphate / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
X-PLOR3.851Brungerstructure solution
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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