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- PDB-2adt: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. -

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Basic information

Entry
Database: PDB / ID: 2adt
TitleNMR structure of a 30 kDa GAAA tetraloop-receptor complex.
Components43-MER
KeywordsRNA / GAAA tetraloop GAAA tetraloop-receptor
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsDavis, J.H. / Tonelli, M. / Scott, L.G. / Jaeger, L. / Williamson, J.R. / Butcher, S.E.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: RNA Helical Packing in Solution: NMR Structure of a 30 kDa GAAA Tetraloop-Receptor Complex
Authors: Davis, J.H. / Tonelli, M. / Scott, L.G. / Jaeger, L. / Williamson, J.R. / Butcher, S.E.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: 43-MER
B: 43-MER


Theoretical massNumber of molelcules
Total (without water)27,7472
Polymers27,7472
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 43-MER


Mass: 13873.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GAAA tetraloop-receptor RNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
2422D NOESY
252HNN-COSY
161(H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1All NMR samples were between 0.5 and 2.0 mM RNA,100% D2O100% D2O
2All NMR samples were between 0.5 and 2.0 mM RNA, 10% D2O, 90 H2O10% D2O, 90 H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1~50 mM NaCl 6.81 atm303 K
2~50 Mm Na Cl 6.81 atm283 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
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004
Varian INOVAVarianINOVA9005

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Biospincollection
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
X-PLOR-NIH2.11Schwieters, C. D., Kuszewski, J. J., Tjandra, N.structure solution
NMRPipe2.3Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G.,processing
Sparky3.111T. D. Goddard and D. G. Knellerdata analysis
X-PLOR-NIH2.11Schwieters, C. D., Kuszewski, J. J., Tjandra, N.refinement
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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