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- PDB-1kp7: Conserved RNA Structure within the HCV IRES eIF3 Binding Site -

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Basic information

Entry
Database: PDB / ID: 1kp7
TitleConserved RNA Structure within the HCV IRES eIF3 Binding Site
ComponentsHepatitis C Virus Internal Ribosome Entry Site Fragment
KeywordsRNA / cytosine mismatch / EIF3 / HCV / internal loop / IRES / S-turn
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsGallego, J. / Klinck, R. / Collier, A.J. / Cole, P.T. / Harris, S.J. / Harrison, G.P. / Aboul-ela, F. / Walker, S. / Varani, G.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: A conserved RNA structure within the HCV IRES eIF3-binding site.
Authors: Collier, A.J. / Gallego, J. / Klinck, R. / Cole, P.T. / Harris, S.J. / Harrison, G.P. / Aboul-Ela, F. / Varani, G. / Walker, S.
History
DepositionDec 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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 Internal Ribosome Entry Site Fragment


Theoretical massNumber of molelcules
Total (without water)9,5961
Polymers9,5961
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 / 26energy-minimized average of 26 converged conformers with low energy and low restraint violations
Representative

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Components

#1: RNA chain Hepatitis C Virus Internal Ribosome Entry Site Fragment


Mass: 9595.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 polymerase RNA synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY, DQF-COSY, TOCSY, H-P HETCOR
1223D C-edited NOESY, (H)CCH COSY, HCP, C-edited H-P HETCOR, C-edited TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM RNA, 10mM sodium phosphate buffer, 0.1mM EDTAD2O or 90% H2O, 10% D2O
20.9 mM U-15N,13C RNA, 10mM sodium phosphate buffer, 0.1mM EDTAD2O or 90% H2O, 10% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate / pH: 6 / Pressure: ambient / Temperature: 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
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX5002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: energy-minimized average of 26 converged conformers with low energy and low restraint violations
Conformers calculated total number: 26 / Conformers submitted total number: 1

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