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- PDB-1p5o: Solution Structure of HCV IRES Domain II -

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Basic information

Entry
Database: PDB / ID: 1p5o
TitleSolution Structure of HCV IRES Domain II
Components77-MER
KeywordsRNA / RIBONUCLEIC ACID / HEPATITIS C VIRUS / INTERNAL RIBOSOME ENTRY SITE / tRNA / LOOP E MOTIF / HAIRPIN LOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / see reference above
AuthorsLukavsky, P.J. / Kim, I. / Otto, G.A. / Puglisi, J.D.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of HCV IRES domain II determined by NMR.
Authors: Lukavsky, P.J. / Kim, I. / Otto, G.A. / Puglisi, J.D.
History
DepositionApr 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: 77-MER


Theoretical massNumber of molelcules
Total (without water)24,7771
Polymers24,7771
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)12 / 200lowest restraint violation and total energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain 77-MER


Mass: 24776.691 Da / Num. of mol.: 1 / Fragment: HCV IRES domain II (residues 45-117) / Source method: obtained synthetically
Details: Synthesized by in vitro transcription from linearized plasmid DNA using T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D S-NOESY
3222D NOESY
332DQF-COSY
3422D HP-COSY
3543D 13C-separated NOESY
3643D HCP
3743D HMQC TOCSY
NMR detailsText: The structure was solved using triple resonance, multidimensional NMR spectroscopy and TROSY-type experiments to measure residual dipolar couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.5mM HCV IRES domain II RNA 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride96% D2O, 4% H2O
20.5-1.5mM HCV IRES domain II RNA 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride100% D2O
30.5-1.5mM HCV IRES domain II RNA U-15N,13C 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride96% D2O, 4% H2O
40.5-1.5mM HCV IRES domain II RNA U-15N,13C 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl, 5mM MgCl2 6.4ambient 288 K
2100mM NaCl, 5mM MgCl2 6.4ambient 298 K
3100mM NaCl, 5mM MgCl2 6.4ambient 303 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 INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarianprocessing
Sparky3Goddard, T.D. & Kneller D.G.data analysis
X-PLOR3.1Brunger, A.T.refinement
CNS1.1Brunger, A.T. et alrefinement
PALES1Zweckstetter, M. & Bax, A.refinement
RefinementMethod: see reference above / Software ordinal: 1 / Details: see reference above
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest restraint violation and total energy
Conformers calculated total number: 200 / Conformers submitted total number: 12

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