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- PDB-2jse: NMR reveals absence of hydrogen bonding in adjacent UU and AG mis... -

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Basic information

Entry
Database: PDB / ID: 2jse
TitleNMR reveals absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.
ComponentsRNA (5'-R(*GP*GP*AP*GP*UP*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*AP*UP*CP*UP*CP*C)-3')
KeywordsRNA / NMR structure of RNA loop 5' GUGG 3' / 3' CUAC 5' / G base flipped out / 2x2 thermodynamics / Lack of hydrogen bonding / Absence of hydrogen bonding / UU internal loop / UU/AG internal loop / AG internal loop / Internal loop from protein L11 binding site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsNMR structure of RNA loop 5' GUGG 3' / 3' CUAC 5'
AuthorsShankar, N.
CitationJournal: Biochemistry / Year: 2007
Title: NMR Reveals the Absence of Hydrogen Bonding in Adjacent UU and AG Mismatches in an Isolated Internal Loop from Ribosomal RNA
Authors: Shankar, N. / Xia, T. / Kennedy, S.D. / Krugh, T.R. / Mathews, D.H. / Turner, D.H.
History
DepositionJul 3, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: 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 29, 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*AP*GP*UP*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*AP*UP*CP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,1121
Polymers7,1121
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 / 20structures with the lowest energy and least distance and angle violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 7112.306 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: T7 polymerase used to transcribe the RNA from a synthetic duplex DNA template

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR structure of RNA loop 5' GUGG 3' / 3' CUAC 5'
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM RNA, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM C13, N15 RNA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMRNA1
0.6 mMRNAC13, N152
Sample conditionsIonic strength: 80 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and least distance and angle violations
Conformers calculated total number: 20 / Conformers submitted total number: 10

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