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- PDB-1fqz: NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL ... -

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Basic information

Entry
Database: PDB / ID: 1fqz
TitleNMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE
ComponentsHEPATITIS C VIRUS IRES DOMAIN IIID
KeywordsRNA / trans wobble G.U pair / S-turn / sarcin-ricin loop / loop E motif / sheared G.A pair / reverse Hoogsteen A.U pair
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data.
AuthorsKlinck, R. / Westhof, E. / Walker, S. / Afshar, M. / Collier, A. / Aboul-ela, F.
CitationJournal: RNA / Year: 2000
Title: A potential RNA drug target in the hepatitis C virus internal ribosomal entry site.
Authors: Klinck, R. / Westhof, E. / Walker, S. / Afshar, M. / Collier, A. / Aboul-Ela, F.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 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: 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: HEPATITIS C VIRUS IRES DOMAIN IIID


Theoretical massNumber of molelcules
Total (without water)8,8001
Polymers8,8001
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)1 / 1structures with acceptable covalent geometry, structures with favorable non-bond energy
Representative

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Components

#1: RNA chain HEPATITIS C VIRUS IRES DOMAIN IIID


Mass: 8800.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Transcribed 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
1222D NOESY
2322D NOESY
2432D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM RNA, 8mM sodium phosphate buffer pH 6.690% H2O/10% D2O
21.2 mM RNA, 8mM sodium phosphate buffer pH 6.6100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
18mM Na phosphate 6.6ambient 278 K
28mM Na phosphate 6.6ambient 298 K
38mM Na phosphate 6.6ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
NMRPipe1.7Delaglioprocessing
Sparky3.66Goddard & Knellerdata analysis
CHARMM25.2Brooks et al.refinement
Insight II97MSIrefinement
RefinementMethod: Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S- ...Method: Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data.
Software ordinal: 1
Details: Motifs (i) to (vi) were obtained from the following sources: (i) idealized A-form coordinates (InsightII, MSI); (ii)&(iii) PDB 430D.pdb; (iv) PDB 1ETG.pdb; (vi) PDB 1QA6.pdb; Motif (v) was constructed manually.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy
Conformers calculated total number: 1 / Conformers submitted total number: 1

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