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- PDB-2f8u: G-quadruplex structure formed in human Bcl-2 promoter, hybrid form -

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Basic information

Entry
Database: PDB / ID: 2f8u
TitleG-quadruplex structure formed in human Bcl-2 promoter, hybrid form
Components5'-D(*GP*GP*GP*CP*GP*CP*GP*GP*GP*AP*GP*GP*AP*AP*TP*TP*GP*GP*GP*CP*GP*GP*G)-3'
KeywordsDNA / G-quadruplex / Bcl-2 promoter
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsDai, J. / Chen, D. / Carver, M. / Yang, D.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region.
Authors: Dai, J. / Chen, D. / Jones, R.A. / Hurley, L.H. / Yang, D.
History
DepositionDec 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*GP*GP*CP*GP*CP*GP*GP*GP*AP*GP*GP*AP*AP*TP*TP*GP*GP*GP*CP*GP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3091
Polymers7,3091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: DNA chain 5'-D(*GP*GP*GP*CP*GP*CP*GP*GP*GP*AP*GP*GP*AP*AP*TP*TP*GP*GP*GP*CP*GP*GP*G)-3'


Mass: 7308.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G-quadruplex of Bcl-2 promoter

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
1222D TOCSY
132DQF-COSY
142PE-COSY
1512D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM DNA oligomer, 20mM potassium phosphate buffer, 40mM potassium chloride, 90% H2O, 10% D2O90% H2O/10% D2O
21mM DNA oligomer, 20mM potassium phosphate buffer, 40mM potassium chloride, 99.99% D2O99.99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
160mM 7.0 1 atm298 K
260mM 7.0 1 atm308 K
360mM 7.0 1 atm288 K
460mM 7.0 1 atm280 K
560mM 7.0 1 atm274 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 Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.refinement
XWINNMR3.5collection
XWINNMR3.5processing
Sparky3.11data analysis
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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