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- PDB-2l8f: Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrot... -

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Basic information

Entry
Database: PDB / ID: 2l8f
TitleStructure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon
Components
  • RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')
  • RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3')
KeywordsRNA / RNA motif / internal loop / 3RRs
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest constraint energy, model 1
AuthorsLerman, Y. / Kennedy, S.D. / Turner, D.H.
CitationJournal: Rna / Year: 2011
Title: NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.
Authors: Lerman, Y.V. / Kennedy, S.D. / Shankar, N. / Parisien, M. / Major, F. / Turner, D.H.
History
DepositionJan 11, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3')
B: RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)7,0672
Polymers7,0672
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)10 / 40no restraint violations; low constraint energy
RepresentativeModel #1lowest constraint energy

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Components

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


Mass: 3522.154 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')


Mass: 3545.194 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
2112D 1H-15N HSQC
2212D 1H-13C HSQC
3312D 1H-13C HSQC
1422D 1H-13C HSQC
2512D 1H-1H NOESY
2612D 1H-1H NOESY
1712D 1H-1H NOESY
1822D 1H-1H NOESY
2922D 1H-1H NOESY
11022D 1H-1H TOCSY
21122D 1H-1H TOCSY
11222D 1H-1H COSY
11322D 31P-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMRNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3')-11
1.5 mMRNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')-21
80 mMsodium chloride-31
10 mMsodium phosphate-41
0.5 mMEDTA-51
1.5 mMRNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3')-62
1.5 mMRNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')-72
80 mMsodium chloride-82
10 mMsodium phosphate-92
0.5 mMEDTA-102
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 6.5 ambient 293 K
20.1 6.5 ambient 273 K
30.1 5 ambient 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
VNMR6.1CVariancollection
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Amberrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 215 / NOE intraresidue total count: 79 / NOE long range total count: 40 / NOE sequential total count: 136
NMR representativeSelection criteria: lowest constraint energy
NMR ensembleConformer selection criteria: no restraint violations; low constraint energy
Conformers calculated total number: 40 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.18 Å
NMR ensemble rmsDistance rms dev: 0.003 Å

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