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- PDB-2aqy: (3+1) assembly of three human telomeric DNA repeats into an asymm... -

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Basic information

Entry
Database: PDB / ID: 2aqy
Title(3+1) assembly of three human telomeric DNA repeats into an asymmetrical dimeric G-quadruplex
Components
  • 5'-D(*GP*(OIP)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'
  • 5'-D(*TP*AP*GP*GP*GP*(DU))-3'
KeywordsDNA / (3+1) G-quadruplex assembly / asymmetric dimeric G-quadruplex / telomeric DNA.
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics matrix relaxation
AuthorsZhang, N. / Phan, A.T. / Patel, D.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: (3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex
Authors: Zhang, N. / Phan, A.T. / Patel, D.J.
History
DepositionAug 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*(OIP)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'
B: 5'-D(*TP*AP*GP*GP*GP*(DU))-3'


Theoretical massNumber of molelcules
Total (without water)6,9002
Polymers6,9002
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 / 10all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*(OIP)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'


Mass: 5050.259 Da / Num. of mol.: 1 / Fragment: three repeats of human telomeric DNA / Mutation: G2(OIP) / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (human).
#2: DNA chain 5'-D(*TP*AP*GP*GP*GP*(DU))-3'


Mass: 1850.226 Da / Num. of mol.: 1 / Fragment: single repeats of human telomeric DNA / Mutation: T22(DU) / Source method: obtained synthetically / Details: T22(DU) mutation

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
142DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1100mM NaCl, 2mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
2100mM NaCl, 2mM phosphate buffer, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM Na+ 6.81 atm303 K
2100mM Na+ 6.81 atm273 K
3100mM Na+ 6.81 atm283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
Felix2000MSIdata analysis
RefinementMethod: distance geometry simulated annealing, molecular dynamics matrix relaxation
Software ordinal: 1
Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 517 restraints, 466 are NOE-derived distance constraints, 22 dihedral angle ...Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 517 restraints, 466 are NOE-derived distance constraints, 22 dihedral angle restraints,51 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable ...Conformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 10 / Conformers submitted total number: 10

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