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Yorodumi- PDB-1whv: Solution structure of the RNA binding domain from hypothetical pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1whv | ||||||
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Title | Solution structure of the RNA binding domain from hypothetical protein BAB23382 | ||||||
Components | poly(A)-specific ribonucleasePoly(A)-specific ribonuclease | ||||||
Keywords | HYDROLASE / 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 / : / 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 | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Authors | Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1whv.cif.gz | 594.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1whv.ent.gz | 516.8 KB | Display | PDB format |
PDBx/mmJSON format | 1whv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/1whv ftp://data.pdbj.org/pub/pdb/validation_reports/wh/1whv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 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 |
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Sample conditions | Ionic strength: 100mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |