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- PDB-1lc6: Solution Structure of the U6 Intramolecular Stem-loop RNA -

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Basic information

Entry
Database: PDB / ID: 1lc6
TitleSolution Structure of the U6 Intramolecular Stem-loop RNA
ComponentsU6 Intramolecular Stem-loop RNA
KeywordsRNA / stem-loop / pentaloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle molecular dynamics, cartesian space simulated annealing, molecular dynamics
AuthorsHuppler, A. / Nikstad, L.J. / Allmann, A.M. / Brow, D.A. / Butcher, S.E.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure.
Authors: Huppler, A. / Nikstad, L.J. / Allmann, A.M. / Brow, D.A. / Butcher, S.E.
History
DepositionApr 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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: U6 Intramolecular Stem-loop RNA


Theoretical massNumber of molelcules
Total (without water)7,6691
Polymers7,6691
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)40 / 100structures with the lowest energy
RepresentativeModel #40lowest energy

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Components

#1: RNA chain U6 Intramolecular Stem-loop RNA


Mass: 7668.615 Da / Num. of mol.: 1 / Mutation: A62G / Source method: obtained synthetically
Details: T7 RNA transcript from synthetic DNA. Sequence occurs in S. cerevisiae.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C-separated NOESY
NMR detailsText: Standard 2D and 3D homonuclear and heteronuclear techniques

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Sample preparation

DetailsContents: 1 mM U6 ISL RNA, 13C15N, pH 7.0, 50 mM NaCl / Solvent system: 100% D2O and 90/10% H2O/D2O
Sample conditionsIonic strength: 50 mM / pH: 7.0 / Pressure: ambient / Temperature: 303 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 DMXBrukerDMX7501
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
DYANA1.5P.Guentert, C.Mumenthaler, T.Herrmannrefinement
Felix98Biosymdata analysis
X-PLOR3.1Axel Brungerstructure solution
Sparky3.72Thomas Goddarddata analysis
RefinementMethod: torsion angle molecular dynamics, cartesian space simulated annealing, molecular dynamics
Software ordinal: 1
Details: Structure based on 521 NOEs, 145 dihedral angles and 25 H-bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 40

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