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- PDB-2m18: Structure of stacked G-quadruplex formed by human TERRA sequence ... -

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Basic information

Entry
Database: PDB / ID: 2m18
TitleStructure of stacked G-quadruplex formed by human TERRA sequence in potassium solution
ComponentsRNA (5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')
KeywordsRNA / RNA G-quadruplex / human telomeric RNA / stacked G-quadruplex
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsMartadinata, H. / Phan, A.T.
CitationJournal: Biochemistry / Year: 2013
Title: Structure of Human Telomeric RNA (TERRA): Stacking of Two G-Quadruplex Blocks in K(+) Solution
Authors: Martadinata, H. / Phan, A.T.
History
DepositionNov 20, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,0964
Polymers13,0964
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
RNA (5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')


Mass: 3273.980 Da / Num. of mol.: 4 / 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-13C HSQC aliphatic
1212D 1H-13C HSQC aromatic
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1512D 1H-1H NOESY
NMR detailsText: The structure was determined using NOE

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Sample preparation

DetailsContents: 1.25 mM RNA (5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.25 mM / Component: RNA (5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')-1
Sample conditionsIonic strength: 90 / 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 and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.peak picking
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
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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