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- PDB-1mnx: The Solution Structure of the Loop E Region of the 5S rRNA from S... -

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Entry
Database: PDB / ID: 1mnx
TitleThe Solution Structure of the Loop E Region of the 5S rRNA from Spinach Chloroplasts.
ComponentsLoop E from 5S rRNA
KeywordsRNA / Loop E / 5S rRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSpinacia oleracea (spinach)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model type detailsminimized average
AuthorsVallurupalli, P. / Moore, P.B.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The Solution Structure of the Loop E Region of the 5S rRNA from Spinach Chloroplasts
Authors: Vallurupalli, P. / Moore, P.B.
#1: Journal: RNA / Year: 1998
Title: The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure
Authors: Leontis, N.B. / Westhof, E.
#2: Journal: Structure / Year: 1997
Title: The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins.
Authors: Dallas, A. / Moore, P.B.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA domain
Authors: Correll, C. / Freeborn, B. / Moore, P.B. / Steitz, T.A.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution
Authors: Lu, M. / Steitz, T.A.
#5: Journal: Embo J. / Year: 1999
Title: The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition
Authors: Stoldt, M. / Wohnert, J. / Ohlenschlager, O. / Gorlach, M. / Brown, L.R.
#6: Journal: Biochemistry / Year: 1988
Title: Higher order structure of chloroplastic 5S ribosomal RNA from spinach.
Authors: Romby, P. / Westhof, E. / Toukifimpa, R. / Mache, R. / Ebel, J.P. / Ehresmann, C. / Ehresmann, B.
History
DepositionSep 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Source and taxonomy
Revision 1.4May 1, 2024Group: Data collection / Database references / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Loop E from 5S rRNA


Theoretical massNumber of molelcules
Total (without water)13,6671
Polymers13,6671
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)13 / 65structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain Loop E from 5S rRNA


Mass: 13667.229 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was in vitro transcribed using T7 RNA polymerase from a linearized plasmid containing the required sequence. The sequence is naturally found in Spinacia oleracea (Spinach) cholorplasts.
Source: (synth.) Spinacia oleracea (spinach)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111(NOESY, HSQC for imino/amino assignments)
221(NOESY, DQF-COSY, HSQC, NOESY-HMQC, (H)CCH COSY, etc. See paper for more details.)
NMR detailsText: This structure was determined using data obtained from homonuclear and heteronuclear experiments.

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Sample preparation

DetailsContents: RNA molecule (1mM-2mM) in 50 mM NaCl, 2.5mM Cacodylate, 0.1mM EDTA, pH 6.0
Solvent system: H2O, D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM 6.0 1 atm298 K
250mM 6.0 1 atm278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
Felix95MSIprocessing
CNS1Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenrefinement
Sparky3Goddard and Knellerdata analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: Distance, Dihedral, Planarity restraints were used in the first round, followed by dipolar couplings in the second round (See paper for details)
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 65 / Conformers submitted total number: 13

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