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- PDB-1idv: NMR structure of HCV ires RNA domain IIIC -

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Basic information

Entry
Database: PDB / ID: 1idv
TitleNMR structure of HCV ires RNA domain IIIC
ComponentsHEPATITIS C IRES RNA DOMAIN IIIC
KeywordsRNA / Hepatitis C RNA / IRES / Stem-loop / Domain IIIC
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics relaxation matrix analysis
AuthorsKaluarachchi, K. / Rijnbrand, R. / Lemon, S.M. / Gorenstein, D.G.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites
Authors: Rijnbrand, R. / Thiviyanathan, V. / Kaluarachchi, K. / Lemon, S.M. / Gorenstein, D.G.
History
DepositionApr 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: HEPATITIS C IRES RNA DOMAIN IIIC


Theoretical massNumber of molelcules
Total (without water)3,2081
Polymers3,2081
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 / 20back calculated data agree with experimental NOESY spectrum
RepresentativeModel #10fewest noe violations

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Components

#1: RNA chain HEPATITIS C IRES RNA DOMAIN IIIC


Mass: 3207.965 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized by in vitro transcription using T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
2422D TOCSY
25231P HETERO-TOCSY
2621H-13C HSQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM Sodium Phosphate buffer, 10 mM KCl, 0.05 mM EDTA, pH 6.890% H2O/10% D2O
210 mM Sodium Phosphate buffer, 10 mM KCl, 0.05 mM EDTA, pH 6.899.996% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM KCl 6.8ambient 283 K
210 mM KCl 6.8ambient 298 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 UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
MORASS2.51POST, MEADOWS, LUXON and GORENSTEINrefinement
RefinementMethod: simulated annealing, molecular dynamics relaxation matrix analysis
Software ordinal: 1
Details: The structures are based on 254 NOE restraints, 12 sugar pucker restraints and 9 hydrogen bonds
NMR representativeSelection criteria: fewest noe violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 20 / Conformers submitted total number: 10

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