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- PDB-1txs: STEM-LOOP D OF THE CLOVERLEAF DOMAIN OF ENTEROVIRAL 5'UTR RNA -

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Basic information

Entry
Database: PDB / ID: 1txs
TitleSTEM-LOOP D OF THE CLOVERLEAF DOMAIN OF ENTEROVIRAL 5'UTR RNA
ComponentsEnteroviral 5'-UTR
KeywordsRNA / TETRALOOP UACG / CLOSING WOBBLE UG PAIR / PYRIMIDINE-PYRIMIDINE MISMATCHES / TWO-NUCLEOTIDE BULGE
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Torsion angle dynamics, restrained molecular dynamics
AuthorsDu, Z. / Yu, J. / Ulyanov, N.B. / Andino, R. / James, T.L.
CitationJournal: Biochemistry / Year: 2004
Title: Solution Structure of a Consensus Stem-Loop D RNA Domain that Plays Important Roles in Regulating Translation and Replication in Enteroviruses and Rhinoviruses
Authors: Du, Z. / Yu, J. / Ulyanov, N.B. / Andino, R. / James, T.L.
History
DepositionJul 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 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: Enteroviral 5'-UTR


Theoretical massNumber of molelcules
Total (without water)12,1231
Polymers12,1231
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)20 / 25LOWEST TOTAL ENERGY
RepresentativeModel #1lowest total energy

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Components

#1: RNA chain Enteroviral 5'-UTR


Mass: 12123.159 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH 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
3222D NOESY
332DQF-COSY
3422D TOCSY
3543D 13C-separated NOESY
1632D H(N)CO
1732D HNN-COSY
2852D CT nondecoupled 13C-HSQC
NMR detailsText: This structure was determined using 541 NOE restraints and 136 RDC restraints.

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM unlabeled RNA, 25 mM sodium chloride, 25 mM sodium phosphate90% H2O, 10% D20
21-2 mM unlabeled RNA, 25 mM sodium chloride, 25 mM sodium phosphateD2O
31-2 mM 13C&15N-labeled RNA, 25 mM sodium chloride, 25 mM sodium phosphate90% H2O, 10% D20
41-2 mM 13C&15N-labeled RNA, 25 mM sodium chloride, 25 mM sodium phosphateD2O
51-2 mM 13C&15N-labeled RNA, 25 mM sodium chloride, 25 mM sodium phosphate, 2.5% (WEIGHT/VOLUME) OF C12E6/N-HEXANOL MIXTURE (MOLAR RATIO 0.64)D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125 mM sodium chloride, 25 mM sodium phosphate 6.5 ambient 278 K
225 mM sodium chloride, 25 mM sodium phosphate 6.5 ambient 298 K
325 mM sodium chloride, 25 mM sodium phosphate 6.5 ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe2.1Delaglioprocessing
Sparky3.1Goddard, Knellerdata analysis
DYANA1.5Guntertrefinement
XPLORNIHBrungerrefinement
RefinementMethod: Torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest total energy
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 25 / Conformers submitted total number: 20

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