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Yorodumi- PDB-3saf: Crystal structure of the human RRP6 catalytic domain with D313N m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3saf | ||||||
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Title | Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site | ||||||
Components | Exosome component 10 | ||||||
Keywords | HYDROLASE / exoribonuclease / RNA exosome | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Januszyk, K. / Liu, Q. / Lima, C.D. | ||||||
Citation | Journal: Rna / Year: 2011 Title: Activities of human RRP6 and structure of the human RRP6 catalytic domain. Authors: Januszyk, K. / Liu, Q. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3saf.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3saf.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 3saf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3saf_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 3saf_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 3saf_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 3saf_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/3saf ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3saf | HTTPS FTP |
-Related structure data
Related structure data | 3sagC 3sahC 2hbjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50354.684 Da / Num. of mol.: 2 / Fragment: UNP residues 180-606 / Mutation: D313N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC10, PMSCL, PMSCL2, RRP6 / Plasmid: PSMT3 SUMO FUSION / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CP RIL References: UniProt: Q01780, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→35 Å / Num. all: 75781 / Num. obs: 75251 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Χ2: 1.511 / Net I/σ(I): 15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HBJ Resolution: 2.5→32.74 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1418335 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.1759 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.24 Å2 / Biso mean: 61.2249 Å2 / Biso min: 26.65 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→32.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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