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- PDB-1fyo: EUKARYOTIC DECODING REGION A-SITE RNA -

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Basic information

Entry
Database: PDB / ID: 1fyo
TitleEUKARYOTIC DECODING REGION A-SITE RNA
ComponentsFRAGMENT OF 18S RIBOSOMAL RNA
KeywordsRNA / stem-internal loop-stem-tetraloop RNA / G-A base pair / bulged A
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsLynch, S.R. / Puglisi, J.D.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structure of a eukaryotic decoding region A-site RNA.
Authors: Lynch, S.R. / Puglisi, J.D.
History
DepositionOct 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRAGMENT OF 18S RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)8,6721
Polymers8,6721
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)25 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #12

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Components

#1: RNA chain FRAGMENT OF 18S RIBOSOMAL RNA


Mass: 8672.185 Da / Num. of mol.: 1
Fragment: 18S RNA - NUCLEOTIDES 1404-1412, 1488-1497 (E. COLI NUMBERS)
Mutation: U1410A, A1490U / Source method: obtained synthetically
Details: This sequence occurs naturally in Tetrahymena thermophila

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
1414D 13C-separated NOESY
151DQF-COSY

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Sample preparation

DetailsContents: 3 mM decoding site RNA, 13C/15N, 10 mM phosphate pH 6.3, 90% H20/10% D20, 100% D20
Solvent system: 90% H2O/10% D20; 100% D2O
Sample conditionsIonic strength: 10 mM / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.83Brungerrefinement
X-PLOR3.83Brungerstructure solution
VNMR6.1processing
Felix6.1processing
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: 682 NOEs, 129 dihedral constraints, 36 Hydrogen bonds
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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