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- PDB-1s34: Solution structure of residues 907-929 from Rous Sarcoma Virus -

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Basic information

Entry
Database: PDB / ID: 1s34
TitleSolution structure of residues 907-929 from Rous Sarcoma Virus
Components5'-R(*GP*GP*GP*GP*AP*GP*UP*GP*GP*UP*UP*UP*GP*UP*AP*UP*CP*CP*UP*UP*CP*CP*C)-3'
KeywordsRNA / stem-loop / tetraloop / bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Simulated annealing. Refinement using torsion angle dynamics, the DELPHIC database
AuthorsCabello-Villegas, J. / Giles, K.E. / Soto, A.M. / Yu, P. / Beemon, K.L. / Wang, Y.X.
CitationJournal: Rna / Year: 2004
Title: Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor.
Authors: Cabello-Villegas, J. / Giles, K.E. / Soto, A.M. / Yu, P. / Mougin, A. / Beemon, K.L. / Wang, Y.X.
History
DepositionJan 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: 5'-R(*GP*GP*GP*GP*AP*GP*UP*GP*GP*UP*UP*UP*GP*UP*AP*UP*CP*CP*UP*UP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3501
Polymers7,3501
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*GP*GP*GP*GP*AP*GP*UP*GP*GP*UP*UP*UP*GP*UP*AP*UP*CP*CP*UP*UP*CP*CP*C)-3'


Mass: 7350.335 Da / Num. of mol.: 1 / Fragment: Pseudo 5'-splice site / Source method: obtained synthetically / Details: In vitro transcription

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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
131DQF-COSY
141HNN-COSY
2522D NOESY
161HCP
NMR detailsText: RDC restraints were obtained for the base one bond H-C and H-N using HSQC experiments. RDC restraints for the ribose were obtained from measurements on an Relay HCCH-COSY (Vallurupalli and ...Text: RDC restraints were obtained for the base one bond H-C and H-N using HSQC experiments. RDC restraints for the ribose were obtained from measurements on an Relay HCCH-COSY (Vallurupalli and Moore, J Biomol NMR. 2002. 24(1):63-6). Anisotropic conditions were ~20 mg/ml pf1 phage.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 23 mer RNA (NRS23)>99% D2O
21 mM NRS2390% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125mM NaCl, 10 mM Sodium Phosphate 6.5ambient 298 K
225mM NaCl, 10 mM Sodium Phosphate 6.5ambient 288 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 DRXBrukerDRX5001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1variancollection
NMRPipe4.1F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Baxprocessing
NMRDraw4.1Delaglio, F.data analysis
NMRView5.0.4Johnson and Blevinsdata analysis
X-PLORNIH 2.0.6C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clorestructure solution
X-PLORNIH 2.0.6C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clorerefinement
RefinementMethod: Simulated annealing. Refinement using torsion angle dynamics, the DELPHIC database
Software ordinal: 1
Details: DELPHIC torsion angle potential was used for the whole molecule. The base position potential was excluded for residues 913, and 917 to 920. Protocol from Clore and Kuszewski (J Am Chem Soc. 2003. 125(6):1518-25)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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