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- PDB-1n66: Structure of the pyrimidine-rich internal loop in the Y-domain of... -

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Entry
Database: PDB / ID: 1n66
TitleStructure of the pyrimidine-rich internal loop in the Y-domain of poliovirus 3'UTR
Componentsinternal loop in the Y-domain of poliovirus 3'UTR
KeywordsRNA / RNA internal loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, conjugate gradient minimization
AuthorsLescrinier, E.M. / Tessari, M. / van Kuppeveld, F.J. / Melchers, W.J. / Hilbers, C.W. / Heus, H.A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure of the Pyrimidine-rich Internal Loop in the Poliovirus 3'-UTR: The Importance of Maintaining Pseudo-2-fold Symmetry in RNA Helices Containing Two Adjacent Non-canonical Base-pairs.
Authors: Lescrinier, E.M. / Tessari, M. / van Kuppeveld, F.J. / Melchers, W.J. / Hilbers, C.W. / Heus, H.A.
History
DepositionNov 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

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Assembly

Deposited unit
A: internal loop in the Y-domain of poliovirus 3'UTR


Theoretical massNumber of molelcules
Total (without water)7,0341
Polymers7,0341
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain internal loop in the Y-domain of poliovirus 3'UTR


Mass: 7034.227 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM RNAD2O
23mM RNAD2O
33mM RNA90% H2O/10% D2O
41-2mM RNA, U-13C,15N, C-13C,15ND2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.8 ambient 288 K
25.5 ambient 288 K
35.5 ambient 273 K
45.5 ambient 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe2.1Delaglioprocessing
XEASY1.2.0ETH-Zurichdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics, conjugate gradient minimization
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: 20

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