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- PDB-1f84: SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIID -

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Entry
Database: PDB / ID: 1f84
TitleSOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIID
ComponentsHCV-1B IRES RNA DOMAIN IIID
KeywordsRNA / Ribonucleic Acid / Hepatitis C virus internal ribosome entry site / Sarcin/Ricin loop / Loop E motif / Hairpin loop / RNA structure
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Simulated annealing, restrained molecular dynamics
AuthorsLukavsky, P.J. / Otto, G.A. / Lancaster, A.M. / Sarnow, P. / Puglisi, J.D.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function.
Authors: Lukavsky, P.J. / Otto, G.A. / Lancaster, A.M. / Sarnow, P. / Puglisi, J.D.
History
DepositionJun 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2000Provider: 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: 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: HCV-1B IRES RNA DOMAIN IIID


Theoretical massNumber of molelcules
Total (without water)9,4511
Polymers9,4511
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)25 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #21closest to the average

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Components

#1: RNA chain HCV-1B IRES RNA DOMAIN IIID


Mass: 9450.667 Da / Num. of mol.: 1
Fragment: HCV IRES RNA DOMAIN IIID (NUCLEOTIDES 252-290 OF GENOMIC HEPATITIS C VIRAL RNA)
Mutation: A252G / Source method: obtained synthetically
Details: Synthesized enzymatically in-vitro using T7 RNA Polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111P31-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY
221P31-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY
2323D HCP, 3D HMQC-TOCSY, 3D C13-edited NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE HCN AND HCP EXPERIMENTS ON N15,C13-LABELLED RNA

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM RNA, non-isotopically labelled10mM sodium phosphate buffer, pH 6.40 96% H2O, 4% D2O or 100% D2O
21mM RNA, U-15N,13C10mM sodium phosphate buffer, pH 6.40 96% H2O, 4% D2O or 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM 6.40 ambient 283 K
210mM 6.40 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
Sparky3.8Goddarddata analysis
RefinementMethod: Simulated annealing, restrained molecular dynamics / Software ordinal: 1 / Details: SEE REFERENCE ABOVE
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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