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- PDB-2jxv: Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. e... -

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Entry
Database: PDB / ID: 2jxv
TitleSolution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans
ComponentsRNA (33-MER)
KeywordsRNA / ASYMMETRIC INTERNAL LOOP / stem-loop / GAAA TETRALOOP / GU MISMATCH / RESIDUAL DIPOLAR COUPLINGS
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsCevec, M. / Thibaudeau, C. / Plavec, J.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans.
Authors: Cevec, M. / Thibaudeau, C. / Plavec, J.
History
DepositionNov 30, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 29, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA (33-MER)


Theoretical massNumber of molelcules
Total (without water)10,6251
Polymers10,6251
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 / 100structures with the lowest energy and least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (33-MER)


Mass: 10625.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription using T7 RNA polymerase and DNA oligonucleotide template.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D 15N-HSQC
1312D 13C-HSQC
1412D DQF-COSY
1512D HNN-COSY
1612D TOSCY
1712D 1H-31P COSY
1812D 15N-IPAP-HSQC
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D 13C-SEPARATED NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-13C; U-15N] RNA, 10 mM sodium phosphate, 20 mM NaCl, 95% H2O/5% D2O95% H2O/5% D2O
22 mM [U-13C; U-15N] RNA, 10 mM sodium phosphate, 20 mM NaCl, 100% D2O100% D2O
31 mM [U-13C; U-15N] RNA, 10 mM sodium phosphate, 20 mM NaCl, 17 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRNA[U-13C; U-15N]1
10 mMsodium phosphate1
20 mMNaCl1
2 mMRNA[U-13C; U-15N]2
10 mMsodium phosphate2
20 mMNaCl2
1 mMRNA[U-13C; U-15N]3
10 mMsodium phosphate3
20 mMNaCl3
17 mg/mLPf1 phage3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM NaCl 6.7ambient 298 K
220 mM NaCl 6.7ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian NMR SystemVarianNMR System8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmanrefinement
Felix2002Accelrys Software Inc.processing
VnmrJ2.1BVariancollection
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: 693 NOE-derived distance restraints, 130 torsion angle restraints, 51 residual dipolar coupling restraints, 32 hydrogen bond restraints and 22 planarity restraints.
NMR constraintsNOE constraints total: 697 / NOE intraresidue total count: 370 / NOE medium range total count: 57 / NOE sequential total count: 270
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy and least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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