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- PDB-2gvo: Solution structure of a purine rich hexaloop hairpin belonging to... -

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Basic information

Entry
Database: PDB / ID: 2gvo
TitleSolution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides
ComponentsGUANOSINE-5'-MONOPHOSPHATE
KeywordsRNA / RNA structure / hairpin structure / G.U wobble pair / hexaloop / 13C/15N-labeled RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsJoli, F. / Bouchemal, N. / Laigle, A. / Hartmann, B. / Hantz, E.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides.
Authors: Joli, F. / Bouchemal, N. / Laigle, A. / Hartmann, B. / Hantz, E.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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 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: GUANOSINE-5'-MONOPHOSPHATE


Theoretical massNumber of molelcules
Total (without water)5,8451
Polymers5,8451
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)21 / 30all 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
RepresentativeModel #1

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Components

#1: RNA chain GUANOSINE-5'-MONOPHOSPHATE


Mass: 5844.515 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D NOESY
1212D NOESY
1313D (H)CCH-COSY
1412D 1H-13C HSQC
151DQF-COSY
161HNN COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM 6.8ambient 298 K
210mM 6.8ambient 274 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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglio, F. et al.data analysis
Sparky3.11Goddard, T.D., Kneller, G.D.data analysis
Felix97data analysis
Amber7Case, D.A. et al.'structure solution
JUMNA12Lavery, R., Zakrzewska, K., Sklenar, Hstructure solution
Amber7CASE, D.A. et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 187 restraints, 84 are sequential and long range internucleotide distances, 85 dihedral angle restraints, 18 sugar puckers restraints and 15 distance ...Details: the structures are based on a total of 187 restraints, 84 are sequential and long range internucleotide distances, 85 dihedral angle restraints, 18 sugar puckers restraints and 15 distance restaints from hydrogen bonds.
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
Conformers calculated total number: 30 / Conformers submitted total number: 21

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