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- PDB-2o32: Solution structure of U2 snRNA stem I from human, containing modi... -

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Basic information

Entry
Database: PDB / ID: 2o32
TitleSolution structure of U2 snRNA stem I from human, containing modified nucleotides
Components5'-R(*(PSU)P*CP*UP*CP*(OMG)P*(OMG)P*CP*CP*(PSU)P*UP*UP*UP*(OMG)P*GP*CP*UP*AP*AP*(OMG)P*A)-3'
KeywordsRNA / Wobble base-pairs / Tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsSashital, D.G. / Venditti, V. / Angers, C.G. / Cornilescu, G. / Butcher, S.E.
CitationJournal: Rna / Year: 2007
Title: Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human.
Authors: Sashital, D.G. / Venditti, V. / Angers, C.G. / Cornilescu, G. / Butcher, S.E.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: 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(*(PSU)P*CP*UP*CP*(OMG)P*(OMG)P*CP*CP*(PSU)P*UP*UP*UP*(OMG)P*GP*CP*UP*AP*AP*(OMG)P*A)-3'


Theoretical massNumber of molelcules
Total (without water)6,3941
Polymers6,3941
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*(PSU)P*CP*UP*CP*(OMG)P*(OMG)P*CP*CP*(PSU)P*UP*UP*UP*(OMG)P*GP*CP*UP*AP*AP*(OMG)P*A)-3'


Mass: 6393.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human U2 snRNA stem I

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
2422D 13C-1H HSQC
NMR detailsText: This structure was determined using standard 2D NOESY, 2D TOCSY, and natural 13C abundance 2D HSQC.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM RNA; 50 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM RNA; 50 mM NaCl; 99.99% D2O99.99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 7ambient 283 K
250 mM NaCl 7ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Delano, Gros, Grossekunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenstructure solution
X-PLOR2.11.0Schwieters, Kuszewski, Tjzndra, Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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