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- PDB-2hua: Solution Structure of CSFV IRES Domain IIa -

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Basic information

Entry
Database: PDB / ID: 2hua
TitleSolution Structure of CSFV IRES Domain IIa
ComponentsCSFV IRES Domain IIa
KeywordsRNA / RNA HAIRPIN
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsLocker, N. / Easton, L.E. / Lukavsky, P.J.
CitationJournal: Embo J. / Year: 2007
Title: HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly.
Authors: Locker, N. / Easton, L.E. / Lukavsky, P.J.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 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: CSFV IRES Domain IIa


Theoretical massNumber of molelcules
Total (without water)12,9191
Polymers12,9191
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)11 / 100lowest restraint violation and total energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain CSFV IRES Domain IIa


Mass: 12918.777 Da / Num. of mol.: 1 / Fragment: residues 70-84 and 111-127 / Source method: obtained synthetically
Details: Prepared 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
1113D 13C-separated NOESY
1213D HMQC TOCSY
1313D HCP
1432D HP-COSY
1532D DQF-COSY
1632D NOESY
2732D HP-COSY
2832D DQF-COSY
2932D NOESY
21022D S-NOESY
31122D S-NOESY
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
11.5mM CSFV IRES domain IIa RNA U-15N,13C, 10mM phosphate buffer, 50mM sodium chloride, 100% D2O100% D2O
21.5mM CSFV IRES domain IIa RNA, 10mM phosphate buffer, 50mM sodium chloride, 96% H2O, 4% D2O96% H2O, 4% D2O
31.5mM CSFV IRES domain IIa RNA, 10mM phosphate buffer, 50mM sodium chloride, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM sodium chloride 6.0 ambient 298 K
250mM sodium chloride 6.0 ambient 288 K
350mM sodium chloride 6.0 ambient 278 K

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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 AVANCEBrukerAVANCE8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORXPLOR-NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
XwinNMR3.1Brukerprocessing
Sparky3Goddard, Knellerdata analysis
PALES1Zweckstetter, Baxrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest restraint violation and total energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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