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- PDB-1jzc: THE SOLUTION STRUCTURE OF THE MUTANT 5'AUG3' TRILOOP IN THE RNA P... -

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Basic information

Entry
Database: PDB / ID: 1jzc
TitleTHE SOLUTION STRUCTURE OF THE MUTANT 5'AUG3' TRILOOP IN THE RNA PROMOTER REGION OF THE BROME MOSAIC VIRUS GENOMIC (+)-RNA
Components5'-R(*GP*GP*UP*GP*CP*AP*UP*GP*GP*CP*AP*CP*C)-3'
KeywordsRNA / Brome Mosaic Virus / BMV / triloop / Replication / Promoter / RNA polymerase
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing restrained molecular dynamics
Model type detailsminimized average
AuthorsKim, C.-H. / Kao, C.C.
Citation
Journal: RNA / Year: 2001
Title: A mutant viral RNA promoter with an altered conformation retains efficient recognition by a viral RNA replicase through a solution-exposed adenine
Authors: Kim, C.-H. / Kao, C.C.
#1: Journal: 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.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: Structural and Thermodynamic Studies on Mutant RNA motifs that impair the Specificity between a Viral Replicase and its Promoter
Authors: Kim, C.-H. / Tinoco Jr., I.
History
DepositionSep 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: 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: 5'-R(*GP*GP*UP*GP*CP*AP*UP*GP*GP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,1731
Polymers4,1731
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 / 17a strucutre averaged over these 17 calculated structures.
Representativeminimized average structure

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Components

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


Mass: 4172.541 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is a mutant triloop of which the wild type is naturally occuring in Brome Mosaic Virus genomic RNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
131DQF-COSY
2412D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM RNA triloop 13mer, 10mM Na Phosphate, pH=6.590% H2O/10% D2O
22 mM RNA triloop 13mer, 10mM Na Phosphate, pH=6.599.96% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM NaCl 6.5ambient 293 K
210 mM NaCl 6.5ambient 283 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 AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Axel Brungerstructure solution
XwinNMRcollection
UXNMRcollection
Felixdata analysis
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: simulated annealing restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: a strucutre averaged over these 17 calculated structures.
Conformers calculated total number: 17 / Conformers submitted total number: 1

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