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- PDB-1ug8: NMR structure of the R3H domain from Poly(A)-specific Ribonuclease -

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Basic information

Entry
Database: PDB / ID: 1ug8
TitleNMR structure of the R3H domain from Poly(A)-specific Ribonuclease
ComponentsPoly(A)-specific RibonucleasePoly(A)-specific ribonuclease
KeywordsHYDROLASE / R3H domain / POLY(A)-SPECIFIC 3'-EXORIBONUCLEASE / PARN / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


KSRP (KHSRP) binds and destabilizes mRNA / : / box H/ACA sno(s)RNA 3'-end processing / Deadenylation of mRNA / poly(A)-specific ribonuclease / telomerase RNA stabilization / poly(A)-specific ribonuclease activity / cation binding / miRNA catabolic process / regulation of telomerase RNA localization to Cajal body ...KSRP (KHSRP) binds and destabilizes mRNA / : / box H/ACA sno(s)RNA 3'-end processing / Deadenylation of mRNA / poly(A)-specific ribonuclease / telomerase RNA stabilization / poly(A)-specific ribonuclease activity / cation binding / miRNA catabolic process / regulation of telomerase RNA localization to Cajal body / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of telomere maintenance via telomerase / postsynapse / nuclear speck / glutamatergic synapse / nucleolus / protein kinase binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
R3H-like domain / Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / Ribonuclease CAF1 / R3H domain / CAF1 family ribonuclease / R3H domain / R3H domain superfamily / R3H domain profile. ...R3H-like domain / Poly(A)-specific ribonuclease, RNA-binding / PARN, R3H domain / RNA binding domain / Ribonuclease CAF1 / R3H domain / CAF1 family ribonuclease / R3H domain / R3H domain superfamily / R3H domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / RNA-binding domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(A)-specific ribonuclease PARN
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsNagata, T. / Muto, Y. / Hayami, N. / Uda, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. ...Nagata, T. / Muto, Y. / Hayami, N. / Uda, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: NMR structure of the R3H domain from Poly(A)-specific Ribonuclease
Authors: Nagata, T. / Muto, Y. / Hayami, N. / Uda, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. ...Authors: Nagata, T. / Muto, Y. / Hayami, N. / Uda, H. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Kobayashi, N. / Tanaka, A. / Osanai, T. / Matsuo, Y. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Yokoyama, S.
History
DepositionJun 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(A)-specific Ribonuclease


Theoretical massNumber of molelcules
Total (without water)9,9441
Polymers9,9441
Non-polymers00
Water0
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 Poly(A)-specific Ribonuclease / Poly(A)-specific ribonuclease


Mass: 9944.077 Da / Num. of mol.: 1 / Fragment: R3H domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: RIKEN cDNA 1200003I18 / Plasmid: P020513-14 / References: UniProt: Q8VDG3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.45mM PROTEIN U-15N, 13C; 50mM phosphate buffer NA; 100mM Na2SO4; 1mM DTT; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7.2 / Pressure: ambient / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnsondata analysis
CYANA1Guentert, P.structure solution
NMRPipe1.8Delaglioprocessing
KUJIRA0.816Kobayashi, N.data analysis
CYANA1Guentert, P.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / 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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