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- PDB-1t28: High resolution structure of a picornaviral internal cis-acting r... -

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Entry
Database: PDB / ID: 1t28
TitleHigh resolution structure of a picornaviral internal cis-acting replication element
Components34-MER
KeywordsRNA / CRE / picornavirus / rhino virus / stem loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, molecular dynamics, simulated annealing
Model type detailsminimized average
AuthorsThiviyanathan, V. / Yang, Y. / Kaluarachchi, K. / Reynbrand, R. / Gorenstein, D.G. / Lemon, S.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: High resolution structure of a picornaviral internal cis-acting replication element(cre).
Authors: Thiviyanathan, V. / Yang, Y. / Kaluarachchi, K. / Reynbrand, R. / Gorenstein, D.G. / Lemon, S.M.
History
DepositionApr 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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: 34-MER


Theoretical massNumber of molelcules
Total (without water)11,0411
Polymers11,0411
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 18averaged structure
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain 34-MER


Mass: 11040.671 Da / Num. of mol.: 1 / Fragment: CRE of the Human Rhinovirus type 14 / Source method: obtained synthetically
Details: The RNA sequence was synthesized using T7 system. The sequence occurs in Human Rhinovirus type 14.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
13115N, and 13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM RNA U-15N,13C, 10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.02 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
21.8 mM RNA, 8-10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.02 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
31.8 mM RNA, 8-10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.4-4 mM Mg2+, 90% H2O, 10% D2O90% H2O/10% D2O
40.8 mM RNA, 15N,13C (only the A residues), 10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.02 mM EDTA, 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.8 ambient 298 K
26.8 ambient 298 K
36.8 ambient 298 K
46.8 ambient 298 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
Varian UNITYPLUSVarianUNITYPLUS6001
Varian UNITYPLUSVarianUNITYPLUS7502

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000MSIprocessing
X-PLOR3.1Brunger, A.T., et al.,refinement
RefinementMethod: distance geometry, molecular dynamics, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: averaged structure / Conformers calculated total number: 18 / Conformers submitted total number: 1

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