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- PDB-2kbp: Solution structure of a G-quadruplex of human telomeric RNA -

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Entry
Database: PDB / ID: 2kbp
TitleSolution structure of a G-quadruplex of human telomeric RNA
Components5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3'
KeywordsRNA / G-quadruplex / parallel form / telomeric
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Distance geometry, simulated annealing, molecular dynamics constrained with NMR data (NOE, dihedral, hydrogen-bond constraints)
AuthorsPhan, A.T. / Martadinata, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution.
Authors: Martadinata, H. / Phan, A.T.
History
DepositionDec 5, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3'
B: 5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3'


Theoretical massNumber of molelcules
Total (without water)7,8192
Polymers7,8192
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3'


Mass: 3909.352 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-13C HSQC
1312D 1H-1H COSY
1412D 1H-1H NOESY
1512D 1H-13C JR HMBC
1612D 1H-1H JR NOESY
171H-D exchange
18115N filtered

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Sample preparation

DetailsContents: 1.25mM telomeric RNA-1, 70 mM potassium chloride-2, 20 mM potassium phosphate-3, 10 % D2O-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.25 mMtelomeric RNA-11
70 mMpotassium chloride-21
20 mMpotassium phosphate-31
10 %D2O-41
Sample conditionsIonic strength: 90 mM K+ / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorestructure solution
RefinementMethod: Distance geometry, simulated annealing, molecular dynamics constrained with NMR data (NOE, dihedral, hydrogen-bond constraints)
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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