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Yorodumi- PDB-2hbm: Structure of the yeast nuclear exosome component, Rrp6p, reveals ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hbm | |||||||||
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Title | Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn, Zn, and UMP | |||||||||
Components | Exosome complex exonuclease RRP6 | |||||||||
Keywords | HYDROLASE / GENE REGULATION / exosome / RNA metabolism / RNA surveillance / RNA processing | |||||||||
Function / homology | Function and homology information 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 / nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process ...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 / nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U4 snRNA 3'-end processing / 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 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / rRNA primary transcript binding / RNA catabolic process / regulation of telomere maintenance / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / single-stranded RNA binding / nucleotide binding / nucleolus / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å | |||||||||
Authors | Midtgaard, S.F. / Assenholt, J. / Jonstrup, A.T. / Van, L.B. / Jensen, T.H. / Brodersen, D.E. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Authors: Midtgaard, S.F. / Assenholt, J. / Jonstrup, A.T. / Van, L.B. / Jensen, T.H. / Brodersen, D.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hbm.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hbm.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hbm_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 2hbm_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | 2hbm_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 2hbm_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/2hbm ftp://data.pdbj.org/pub/pdb/validation_reports/hb/2hbm | HTTPS FTP |
-Related structure data
Related structure data | 2hbjSC 2hbkC 2hblC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the monomer present in the asymmetric unit. |
-Components
#1: Protein | Mass: 47675.125 Da / Num. of mol.: 1 / Fragment: Rrp6p central fragment, residues 129-536 / Mutation: Y361A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RRP6 / Plasmid: pET30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-U5P / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12-14% PEG 20000, 0.1M Mes or Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 9, 2006 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.61 Å / Num. all: 15522 / Num. obs: 15522 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 71.43 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.952 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible obs: 92.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1416 / Num. unique obs: 1416 / Χ2: 0.944 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2HBJ Resolution: 2.7→29.61 Å / FOM work R set: 0.796 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.61 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29
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Xplor file |
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