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- PDB-2ro2: Solution structure of domain I of the negative polarity CChMVd ha... -

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Basic information

Entry
Database: PDB / ID: 2ro2
TitleSolution structure of domain I of the negative polarity CChMVd hammerhead ribozyme
ComponentsRNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')
KeywordsRNA / hammerhead ribozyme / viroid / CCHMVD / heptaloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, restrained energy minimization
Model type detailsminimized average
AuthorsGallego, J. / Dufour, D. / Gago, S. / de la Pena, M. / Flores, R.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads
Authors: Dufour, D. / de la Pena, M. / Gago, S. / Flores, R. / Gallego, J.
History
DepositionMar 5, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 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*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,4351
Polymers7,4351
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 / 100Structures with the least restraint violations and total energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 7435.457 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
2422D 1H-1H NOESY
1532D 1H-15N HSQC
1632D HNN COSY
1742D 1H-13C HSQC
1843D NOESY-HMQC
1943D (H)CCH ECOSY
11042D (H)CCH-TOCSY
11143D HCP
11243D 13C-ED-1H-31P HETCOR
11343D HCP-CCH TOCSY
11442D HCNCH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 100% D2O100% D2O
20.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31mM [U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
40.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')1
10 mMsodium phosphate1
0.1 mMEDTA1
1 mMRNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')2
10 mMsodium phosphate2
0.1 mMEDTA2
1 mMRNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')[U-100% 15N]3
10 mMsodium phosphate3
0.1 mMEDTA3
1 mMRNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')[U-100% 13C; U-100% 15N]4
10 mMsodium phosphate4
0.1 mMEDTA4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
112.4 6 ambient 297 K
212.4 6 ambient 281 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
Sparky3.11Goddarddata analysis
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollmrefinement
RefinementMethod: simulated annealing, restrained energy minimization / Software ordinal: 1
Details: minimized average structure of 29 converged conformers with the least restraint violation energy and total energy
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: Structures with the least restraint violations and total energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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