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Yorodumi- PDB-2cpr: Solution structure of the HRDC domain of human Exosome component 10 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cpr | ||||||
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Title | Solution structure of the HRDC domain of human Exosome component 10 | ||||||
Components | Exosome component 10 | ||||||
Keywords | GENE REGULATION / HRDC / helix-bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information nucleolar exosome (RNase complex) / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / positive regulation of mRNA cis splicing, via spliceosome / regulation of telomerase RNA localization to Cajal body / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / RNA exonuclease activity ...nucleolar exosome (RNase complex) / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / positive regulation of mRNA cis splicing, via spliceosome / regulation of telomerase RNA localization to Cajal body / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / RNA exonuclease activity / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / nuclear mRNA surveillance / RNA catabolic process / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process / negative regulation of telomere maintenance via telomerase / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / small-subunit processome / euchromatin / rRNA processing / ribosomal small subunit biogenesis / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / single-stranded RNA binding / DNA repair / nucleotide binding / nucleolus / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dyanamics, 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 HRDC domain of human Exosome component 10 Authors: Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX Determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cpr.cif.gz | 760.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cpr.ent.gz | 639 KB | Display | PDB format |
PDBx/mmJSON format | 2cpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cpr_validation.pdf.gz | 343.2 KB | Display | wwPDB validaton report |
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Full document | 2cpr_full_validation.pdf.gz | 481.4 KB | Display | |
Data in XML | 2cpr_validation.xml.gz | 41 KB | Display | |
Data in CIF | 2cpr_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/2cpr ftp://data.pdbj.org/pub/pdb/validation_reports/cp/2cpr | HTTPS FTP |
-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: 13945.032 Da / Num. of mol.: 1 / Fragment: HRDC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: EXOSC10 / Plasmid: P040906-09 / References: UniProt: Q01780 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.45mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dyanamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |