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- PDB-1s9l: NMR Solution Structure of a Parallel LNA Quadruplex -

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Basic information

Entry
Database: PDB / ID: 1s9l
TitleNMR Solution Structure of a Parallel LNA Quadruplex
Components5'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3'
KeywordsRNA / LNA / QUADRUPLEX
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRandazzo, A. / Esposito, V. / Ohlenschlager, O. / Ramachandran, R. / Mayola, L.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: NMR solution structure of a parallel LNA quadruplex.
Authors: Randazzo, A. / Esposito, V. / Ohlenschlager, O. / Ramachandran, R. / Mayola, L.
History
DepositionFeb 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 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'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3'
B: 5'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3'
C: 5'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3'
D: 5'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3'


Theoretical massNumber of molelcules
Total (without water)6,7644
Polymers6,7644
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)20 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: RNA chain
5'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3'


Mass: 1691.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence contains all LNA residues

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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
1421H-31P 2D COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.80 mM, 5'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3', 10 mM KH2PO4, 70 mM KCl, 0.2 mM EDTA, H2O/D2O 9:1H2O/D2O 9:1
21.80 mM, 5'-((TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3', 10 mM KH2PO4, 70 mM KCl, 0.2 mM EDTA, D2OD2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR970101Brukercollection
VNMR6.1/CVariancollection
Felix98Accelrysprocessing
CYANA1.0.6Guentertstructure solution
Discover98Accelrysrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 292 (73 per strand) NOE-derived distance constraints, 48 hydrogen bonds constraints, 36 (9 per strand) dihedral angle restraints. The 20 structures with the lowest CYANA target functions ...Details: 292 (73 per strand) NOE-derived distance constraints, 48 hydrogen bonds constraints, 36 (9 per strand) dihedral angle restraints. The 20 structures with the lowest CYANA target functions were subjected energy minimization (with no angle constraints) using the conjugate gradient method and the CVFF force field
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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