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- PDB-1ju7: NMR Solution Structure of the RNA Hairpin Binding Site for the Hi... -

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Basic information

Entry
Database: PDB / ID: 1ju7
TitleNMR Solution Structure of the RNA Hairpin Binding Site for the Histone Stem-loop Binding Protein
Components5'-R(*GP*GP*CP*CP*AP*AP*AP*GP*GP*CP*CP*CP*UP*UP*UP*UP*CP*AP*GP*GP*GP*CP*CP*AP*CP*CP*CP*A)-3'
KeywordsRNA / hairpin / tetraloop / 3' stack
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsDeJong, E.S. / Marzluff, W.F. / Nikonowicz, E.P.
CitationJournal: RNA / Year: 2002
Title: NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.
Authors: DeJong, E.S. / Marzluff, W.F. / Nikonowicz, E.P.
History
DepositionAug 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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: 5'-R(*GP*GP*CP*CP*AP*AP*AP*GP*GP*CP*CP*CP*UP*UP*UP*UP*CP*AP*GP*GP*GP*CP*CP*AP*CP*CP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)8,9281
Polymers8,9281
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 / 60structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #5closest to the average

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Components

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


Mass: 8928.382 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally at the 3' end of the replication-dependent histone mRNAs of vertebrates. This sequence corresponds to the mouse H4-12 gene.
References: GenBank: 51308

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
114NOESY
1213D 13C-separated NOESY
2323D 15N-separated NOESY
3433D 13C-separated NOESY
152DQF-COSY
164HETCOR
NMR detailsText: This structure was determined using a variety of 2D and 3D homo- and hetero-nuclear NMR methods.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.3 mM U-13C; 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8100% D2O
22.5 mM U-15N; 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.810% D2O, 90% H2O
32.0 mM U-13C,C5-2H; 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8100% D2O
42.8 mM unlabeled 20 mM KPi, 20 mM KCl, 0.02 mM EDTA, pH 6.8100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM 6.8ambient 301 K
2100 mM 6.8ambient 280 K
3100 mM 6.8ambient 301 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 spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix980MSI-Biosymprocessing
X-PLOR3.851Brunger, A.refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Calculations were performed using 232 conformationally restrictive NOE derived distance constraints and 55 backbone and 15 ribose torsion angle constraints. Base pair constraints were ...Details: Calculations were performed using 232 conformationally restrictive NOE derived distance constraints and 55 backbone and 15 ribose torsion angle constraints. Base pair constraints were introduced for six base pairs using heavy atom-heavy atom constraints. Coordinates are for the hairpin domain only. 5' flanking (ggccaaa) and 3' flanking (accca) coordinates are not included with this deposition. Few constraints were obtained for these very dynamic regions and although they were included as part of the structure calculation, their conformations appear to be randomly distributed.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10

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