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- PDB-1whv: Solution structure of the RNA binding domain from hypothetical pr... -

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Basic information

Entry
Database: PDB / ID: 1whv
TitleSolution structure of the RNA binding domain from hypothetical protein BAB23382
Componentspoly(A)-specific ribonucleasePoly(A)-specific ribonuclease
KeywordsHYDROLASE / RNA recognition motif / RRM / RNA binding domain / RBD / RNP / poly(A)-specific ribonuclease / PARN / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


KSRP (KHSRP) binds and destabilizes mRNA / ncRNA deadenylation / box H/ACA RNA 3'-end processing / Deadenylation of mRNA / miRNA catabolic process / poly(A)-specific ribonuclease / telomerase RNA stabilization / cation binding / poly(A)-specific ribonuclease activity / regulation of telomerase RNA localization to Cajal body ...KSRP (KHSRP) binds and destabilizes mRNA / ncRNA deadenylation / box H/ACA RNA 3'-end processing / Deadenylation of mRNA / miRNA catabolic process / poly(A)-specific ribonuclease / telomerase RNA stabilization / cation binding / poly(A)-specific ribonuclease activity / regulation of telomerase RNA localization to Cajal body / polyadenylation-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 / positive regulation of telomerase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / 3'-5'-exoribonuclease activity / nuclear speck / nucleolus / protein kinase binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
PARN, R3H domain / RNA binding domain / Poly(A)-specific ribonuclease, RNA-binding / R3H domain / Ribonuclease CAF1 / CAF1 family ribonuclease / R3H domain profile. / R3H domain superfamily / R3H domain / RRM (RNA recognition motif) domain ...PARN, R3H domain / RNA binding domain / Poly(A)-specific ribonuclease, RNA-binding / R3H domain / Ribonuclease CAF1 / CAF1 family ribonuclease / R3H domain profile. / R3H domain superfamily / R3H domain / RRM (RNA recognition motif) domain / RNA-binding domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 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. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the RNA binding domain from hypothetical protein BAB23382
Authors: Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: poly(A)-specific ribonuclease


Theoretical massNumber of molelcules
Total (without water)11,0131
Polymers11,0131
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 / deadenylation nuclease / hypothetical protein BAB23382


Mass: 11013.168 Da / Num. of mol.: 1 / Fragment: RNA recognition motif
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: P031020-39 / 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: 0.94mM PROTEIN U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.0 / Pressure: ambient / Temperature: 298 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
CYANA2Guentertstructure solution
NMRPipe2.3Delaglioprocessing
KUJIRA0.901Kobayashi, N.data analysis
CYANA2Guentertrefinement
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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