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- PDB-2kez: NMR structure of U6 ISL at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 2kez
TitleNMR structure of U6 ISL at pH 8.0
ComponentsRNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')
KeywordsRNA / U6 RNA / stem loop / bulge / internal loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsVenditti, V. / Butcher, S.E.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.
Authors: Venditti, V. / Clos, L. / Niccolai, N. / Butcher, S.E.
#1: Journal: Rna / Year: 2003
Title: Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.
Authors: Reiter, N.J. / Nikstad, L.J. / Allmann, A.M. / Johnson, R.J. / Butcher, S.E.
#2: Journal: Biochemistry / Year: 2004
Title: Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change.
Authors: Reiter, N.J. / Blad, H. / Abildgaard, F. / Butcher, S.E.
History
DepositionFeb 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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: RNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,6691
Polymers7,6691
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)10 / 12structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 7668.615 Da / Num. of mol.: 1 / Mutation: A62G / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
1312D 1H-1H TOCSY
143J-MODULATED (13C 1H) CT-HSQC
153J-MODULATED (13C 1H) CT-HSQC
1632D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM RNA, 100% D2O100% D2O
22 mM RNA, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 13C] RNA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')-11
2 mMRNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')-22
0.5 mMRNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')-3[U-100% 13C]3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1508ambient 303 K
2508ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, D. et al.refinement
NMRPipeDelaglio, F. et al.processing
SparkyGoddard, T. et al.chemical shift assignment
XwinNMRBruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 12 / Conformers submitted total number: 10

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