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- PDB-1s2f: Average solution structure of a pseudo-5'-splice site from the ne... -

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Basic information

Entry
Database: PDB / ID: 1s2f
TitleAverage solution structure of a pseudo-5'-splice site from the negative regulator of splicing of 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 / NRS / U1 snRNP binding site / 5' splice site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Simulated annealing. Torsion angle dynamics in refinement.
Model type detailsminimized average
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 8, 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)1 / -
RepresentativeModel #1minimized average structure

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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
131HNN-COSY
141DQF-COSY
NMR detailsText: Exchangeable proton spectra collected at 15 Celsius

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Sample preparation

DetailsContents: RNA Residues 907-929 from NRS (NRS23) / Solvent system: 10 mM Sodium Phosphate, 25 mM NaCl, pH 6.5
Sample conditionsIonic strength: 25 mM NaCl, 10 mM NaPi / pH: 6.5 / Pressure: ambient / Temperature: 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 INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003
Bruker DRXBrukerDRX5004

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIHxplor-nih-2.0.6C.D. Schwieters, J.J. Kuszewski,N. Tjandra, and G.M. Clorerefinement
NMRPipe4.1F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Baxdata analysis
VNMR6.1Cvarian inc.collection
NMRView5.0.4Johnson, B.A.data analysis
RefinementMethod: Simulated annealing. Torsion angle dynamics in refinement.
Software ordinal: 1
Details: 100 structurews were calculated, the minimized average from the 15 lowest energy structures is presented. Constraints used: 423 distance, 63 torsion angle, 117 orientation (RDC). The DELPIC ...Details: 100 structurews were calculated, the minimized average from the 15 lowest energy structures is presented. Constraints used: 423 distance, 63 torsion angle, 117 orientation (RDC). The DELPIC database was employed in the refinement as follows: torsion angle database active for all residues, base-base positional database active for residues 907-912, 914-916, and 921-929. DELPHIC database reference: Clore, G.M. Kuszewski, J. J. Am. Chem. Soc. 125: 1518-1525
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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