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- PDB-1esh: THE SOLUTION STRUCTURE OF THE STEM LOOP C 5'AUA3' TRILOOP OF BROM... -

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Entry
Database: PDB / ID: 1esh
TitleTHE SOLUTION STRUCTURE OF THE STEM LOOP C 5'AUA3' TRILOOP OF BROME MOSAIC VIRUS (+) STRAND RNA
ComponentsRNA (5'-R(*GP*GP*UP*GP*CP*AP*UP*AP*GP*CP*AP*CP*C)-3')
KeywordsRNA / TRILOOP / STEM-LOOP / Brome Mosaic Virus
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / RMD WITH SIMULATED ANNEALING
AuthorsKim, C.-H. / Kao, C.C. / Tinoco Jr., I.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: RNA motifs that determine specificity between a viral replicase and its promoter.
Authors: Kim, C.H. / Kao, C.C. / Tinoco Jr., I.
History
DepositionApr 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: RNA (5'-R(*GP*GP*UP*GP*CP*AP*UP*AP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,1571
Polymers4,1571
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)1 / 22LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

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


Mass: 4156.541 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SEQUENCE OCCURS NATURALLY IN BROME MOSAIC VIRUS EXCEPT FOR THE TERMINAL TWO GC BPS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111H2ONOESY
121D2ONOESY
131(H)CCH-TO
NMR detailsText: THE SUBMITTED STRUCTURE IS THE AVERAGE AND ENERGY MINIMIZED

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Sample preparation

DetailsContents: RNA IN AQUEOUS SOLUTION
Sample conditionsIonic strength: 50mM NACL / pH: 6.5 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1A.T.BRUNGERrefinement
X-PLOR3.1A.T.BRUNGERstructure solution
RefinementMethod: RMD WITH SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 22 / Conformers submitted total number: 1

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