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- PDB-2kjm: Solution structure of SLBP RNA binding domain fragment -

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Basic information

Entry
Database: PDB / ID: 2kjm
TitleSolution structure of SLBP RNA binding domain fragment
ComponentsHistone RNA hairpin-binding protein
KeywordsRNA BINDING PROTEIN / SLBP / histone mRNA / Stem-Loop Binding Protein / Hairpin Binding Protein / mRNA processing / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / histone pre-mRNA DCP binding / histone pre-mRNA 3'end processing complex / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of the SLBP Dependant Mature mRNA / RNA Polymerase II Transcription Termination / mRNA transport ...histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / histone pre-mRNA DCP binding / histone pre-mRNA 3'end processing complex / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of the SLBP Dependant Mature mRNA / RNA Polymerase II Transcription Termination / mRNA transport / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone RNA stem-loop-binding protein SLBP1/SLBP2 / Histone RNA hairpin-binding protein, RNA-binding domain / SLBP, RNA-binding domain superfamily / Histone RNA hairpin-binding protein RNA-binding domain
Similarity search - Domain/homology
Histone RNA hairpin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsThapar, R.
CitationJournal: Biochemistry / Year: 2012
Title: Interaction of the histone mRNA hairpin with stem-loop binding protein (SLBP) and regulation of the SLBP-RNA complex by phosphorylation and proline isomerization.
Authors: Zhang, M. / Lam, T.T. / Tonelli, M. / Marzluff, W.F. / Thapar, R.
History
DepositionJun 3, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone RNA hairpin-binding protein


Theoretical massNumber of molelcules
Total (without water)3,6681
Polymers3,6681
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Histone RNA hairpin-binding protein / Histone stem-loop-binding protein


Mass: 3668.141 Da / Num. of mol.: 1 / Fragment: UNP residues 129-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLBP, HBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q14493

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the N-terminal 30 residue peptide from the RNA binding and processing domain of Stem-Loop Binding Protein (SLBP) that binds a 26 nucleotide hairpin in the 3' untranslated region of histone mRNAs.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1-7 mM SLBP30mer-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: SLBP30mer-1 / Conc. range: 1-7
Sample conditionsIonic strength: 0.05 / pH: 5 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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