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- PDB-1k4a: STRUCTURE OF AGAA RNA TETRALOOP, NMR, 20 STRUCTURES -

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Entry
Database: PDB / ID: 1k4a
TitleSTRUCTURE OF AGAA RNA TETRALOOP, NMR, 20 STRUCTURES
Components5'-R(*GP*GP*UP*UP*CP*AP*GP*AP*AP*GP*AP*AP*CP*C)-3'
KeywordsRNA / Ribonucleic Acid / Tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsWu, H. / Yang, P.K. / Butcher, S.E. / Kang, S. / Chanfreau, G. / Feigon, J.
CitationJournal: EMBO J. / Year: 2001
Title: A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III.
Authors: Wu, H. / Yang, P.K. / Butcher, S.E. / Kang, S. / Chanfreau, G. / Feigon, J.
History
DepositionOct 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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:
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Assembly

Deposited unit
A: 5'-R(*GP*GP*UP*UP*CP*AP*GP*AP*AP*GP*AP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,5101
Polymers4,5101
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 #1this is the lowest energy structure

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Components

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


Mass: 4509.771 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: An RNA Hairpin with AGAA Tetraloop, the primary recognition site for S. cerevisiae RNase III.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2343D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM RNA hairpin, 10mM NaCl, pH 6.3, 90% H2O, 10% D2O90% H2O/10% D2O
22mM RNA hairpin, 10mM NaCl, pH 6.3, 90% H2O, 10% D2O99.99%D2o
31mM 13C/15N labeled RNA hairpin, 10mM NaCl, pH 6.3, 99.99% D2O90% H2O/10% D2O
41mM 13C/15N labeled RNA hairpin,10mM NaCl, pH 6.3, 99.99% D2O99.99%D2o
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM 6.31 atm274 K
210mM 6.31 atm293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker AMXBrukerAMX5002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Felix2000MSIdata analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 326 restraints, 300 are NOE-derived distance restraints, 54 dihedral angle restraints. Additional 26 distance restraints from hydrogen bonds are used in the stem region.
NMR representativeSelection criteria: this is the lowest energy structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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